How a Respected Pediatrician Lost His Medical License — Because He Supported Informed Consent

How a Respected Pediatrician Lost His Medical License — Because He Supported Informed Consent
On Dec. 3, 2020, the Oregon Medical Board issued an “emergency order” to suspend the license of Dr. Paul Thomas, a pediatrician, who along with science writer Jennifer Margulis, Ph.D., co-authored “The Vaccine-Friendly Plan.”

by Jeremy R. Hammond, The Defender
June 14, 2021


On Dec. 3, 2020, the Oregon Medical Board issued an “emergency order” to suspend the license of Dr. Paul Thomas, a pediatrician, who along with science writer Jennifer Margulis, Ph.D., co-authored “The Vaccine-Friendly Plan.”

Affectionately known by his patients and peers as “Dr. Paul,” Thomas was accused by the board of posing a threat to public health by pushing parents to accept his alternative vaccine schedule rather than the routine childhood vaccine schedule recommended by the Centers for Disease Control and Prevention (CDC).

The apparent impetus for the “emergency” meeting, however, was the publication just days prior of a study showing that compared with his vaccinated patients, those patients who received no vaccines have significantly lower incidence of diagnoses and office visits for a broad range of chronic health conditions — including asthmaallergies, eczema, dermatitis, hives, anemia, eye disorders, ear infections, respiratory infections, other infections, breathing issues, behavioral issues, and attention deficit hyperactivity disorder (ADHD).

Thomas obtained institutional review board approval to use his de-identified patient data for research and publication of the study, which was co-authored by James Lyons-Weiler, Ph.D.

The study population consisted of all patients born into his practice. Titled “Relative Incidence of Office Visits and Cumulative Rates of Billed Diagnoses Along the Axis of Vaccination,” it was published in the International Journal of Environmental Research and Public Health on Nov. 22, 2020.

While the study does not demonstrate that vaccination was the cause of the higher incidence and severity of chronic illnesses among vaccinated children, the results do demonstrate to a reasonable degree of certainty that Thomas’ unvaccinated children are healthier and place less of a burden on the healthcare system.

Among patients born into his practice, the rate of autism was one-fifth that of the CDC’s estimated national prevalence of 1 in 54 children. For ADHD, there were zero cases among his unvaccinated patients compared with 5.3% of the variably vaccinated, which in turn compares with the U.S. national rate, according to the CDC, of 9.4%.

Looking at diagnoses for diseases CDC-recommended vaccines are intended to protect against, the study’s authors found a total of 41:29 for varicella (or chicken pox), 10 for pertussis (or whooping cough), and two for rotavirus. The numbers of diagnoses for the unvaccinated group were 23, nine and two, respectively.

These numbers indicated that 17.2 children born into his practice needed to be vaccinated in order for one child to receive the benefit of protection against a vaccine-targeted disease.

To put it another way, for every 17 children vaccinated, 16 received no benefit from having undergone a risk-carrying pharmaceutical intervention. There were zero deaths in Thomas’s practice from any disease for which the CDC recommends vaccination.

Figure 5 of the study compares cumulative office visits per condition in the vaccinated (orange) with unvaccinated (blue) patients over time (days of life).

Importantly, in a letter of complaint dated Dec. 26, 2018, the Oregon Medical Board had requested Thomas produce peer-reviewed evidence to support his alternative approach to vaccination. Yet when he did so, the board dismissed the evidence, clearly demonstrating there was no public health emergency arising from his approach to vaccination.

Just as importantly, the medical board itself, while placing that burden of proof on Thomas, is incapable of producing peer-reviewed evidence demonstrating children vaccinated according to the CDC’s schedule are healthier than children who remained completely unvaccinated.

As the Institute of Medicine (IOM) acknowledged in a 2013 review, “No studies have compared the differences in health outcomes … between entirely unimmunized populations of children and fully immunized children.”

The IOM reiterated that “existing research has not been designed to test the entire immunization schedule” and “studies designed to examine the long-term effects of the cumulative number of vaccines or other aspects of the immunization schedule have not been conducted.”

The Oregon Medical Board’s “emergency” suspension order accused Thomas of “bullying” patients into accepting an alternative vaccine schedule, but this is demonstrably false.

First, it logically cannot be the case that the medical board is opposed to physicians bullying patients. This is evident in the fact that doctors across the state pressure parents to vaccinate strictly according to the CDC’s schedule, and some go so far in their bullying as to expel from their practice families who decline to do so.

Far from the medical board suspending the license of doctors who engage in such behavior, it is evident from the suspension order itself this is precisely the behavior the medical board expects from licensed physicians.

Second, it logically cannot be the case that Thomas pressures parents to accept the alternative schedule presented in his book, “The Vaccine-Friendly Plan,” because that would be contrary to the whole principle — which is that a risk-benefit analysis is required for each vaccine and each individual.

The specific schedule described in the book is merely one possible approach designed to reduce children’s cumulative exposure to aluminum, a known neurotoxin used in vaccines as an adjuvant, which is a substance intended to provoke a stronger immune response.

The board has accused Thomas of pressuring parents into an alternative one-size-fits-all schedule, which is anathema to the whole concept of taking an individualized approach.

The cognitive dissonance of the medical board is illustrated in the fact that the board’s suspension order accuses Thomas of not administering vaccines he recommends in his book. Thus, it logically cannot be true the reason these children did not receive those vaccines is because Thomas pressured them out of it.

The truth is families have flocked to Thomas’s practice in Portland, Oregon precisely because they do not want to be bullied into accepting a one-size-fits-all approach to vaccination. They go to him precisely because he is well known in the community for respecting their right to informed consent.

Thomas’ journey of awakening

Paul Thomas was born in Portland in 1957. In 1961, his family moved to a village in what was then the British territory of Rhodesia on the northern border of South Africa, where Zimbabwe exists today. They were the only white people living in the village.

In 1964, a party came into power in Rhodesia that opposed transition to democratic rule, which would mean the end of rule by a white minority. The regime implemented a policy of apartheid-like segregation and was never internationally recognized.

In 1966, when it was discovered Thomas was attending the village school, he was removed to an all-white school, where he excelled in academics and sports and was eventually given the titular honor of “Head Boy.”

In 1968, the regime held a ceremony to lower the Union Jack and raise the new Rhodesian flag in its place. At school, 11-year-old Thomas was expected to perform this ceremony in keeping with his duty as Head Boy. Considering the new government to be an unlawful regime, he refused. In 1973, at age 15, he was arrested for distributing educational materials the regime deemed “revolutionary.”

Paul Thomas grew up in the former British territory of Rhodesia, located in southern Africa where Zimbabwe is today. Photo credit: Paul Thomas

In 1974, Thomas returned to the U.S. and entered medical school, earning his M.D. at Dartmouth Medical School. He moved back to Portland in 1988, and in 1993, joined a private group practice. In 1986, he adopted his first child and today is the father of nine children — three biological and six adopted.

Thomas says his children were fully vaccinated. At the private group practice, he did things the way he was trained to. “I come from a background of not being aware of vaccine risk,” Thomas explained. “I come from a background of being very well trained that vaccines are ‘safe and effective.’ I believed it.”

He attributes his initial awakening to having read the study by Andrew Wakefield, published in The Lancet in 1998.

While the media constantly report Wakefield’s paper fraudulently claimed to have found an association between the measles, mumps and rubella (MMR) vaccine and autism, in fact, Wakefield and his co-authors explicitly stated they did not show an association. Rather, they relayed the concern of parents that their children developmentally regressed after receiving the MMR vaccine, and hypothesized there might be a link. They called for further studies to examine this question.

The main finding of the paper was that 12 children who had a developmental disorder also had a gastrointestinal disorder. Today, the connection between gut disorders and autism is well established, with much research now focusing on questions such as the role of the gut microbiome in relation to neurological disorders.

Notably, the media never credit Wakefield for pioneering research into this area.

In 2010, The Lancet retracted Wakefield’s paper after the UK’s General Medical Council (GMC) had stripped Wakefield and his co-author, John Walker-Smith, of their medical licenses.

Walker-Smith, senior author of the study, was the gastroenterologist who examined the children. The stated reason for the retraction was that the GMC had judged the authors to have falsely stated the children were “consecutively referred” and their investigation with the children was not approved by the local ethics committee.

The GMC did not charge the authors with fraud but “professional misconduct.” What the mainstream media failed to ever mention in their coverage of the study is that Walker-Smith appealed the GMC’s decision and won. He was reinstated in 2012, with the High Court of Justice ruling the GMC’s charges against him were “untenable” and unsupported by the evidence.

The children in the study were indeed referred successively, rather than as a single batch, and they did not require ethics approval for the procedures the children underwent under Walker-Smith’s care because the procedures were clinically indicated for diagnostic purposes.

Wakefield did not join his co-author in appealing because the legal costs were not covered by his insurance carrier.

Thomas credits Wakefield with awakening him to the possibility vaccines could cause long-term harms. He began attending educational conferences and digging deeply into the medical literature. Then he observed four of his own patients regress into autism after vaccinations, with one case per year starting in 2004.

The fourth such case struck him hard. “That was the last straw for me,” Thomas recalled. “I just couldn’t go on with business as usual.”

The experience led to what he described as his “divorce” with the private group practice. The other physicians there felt it would be unethical to do anything other than what they were told by the CDC. Thomas felt it was unethical for him to continue the “standard of care” practice of treating vaccination as a one-size-fits-all solution.

Thomas left to open his own practice, Integrative Pediatrics, on the founding principles of providing individualized care and respecting his patients’ right to informed consent. He says more than 1,500 patients left with him, and the practice quickly grew to more than 15,000, with a staff of more than 30.

Thomas’ clinic attracted many parents whose children had developed chronic health conditions or developmental disorders and who were wary of further vaccinating according to the CDC’s recommendations. He began noticing a marked difference in the health of patients whose parents were choosing not to follow the CDC’s schedule.

“We started seeing that our less-vaccinated or unvaccinated children seemed to be healthier,” he said. “I mean, it was palpable — you could just tell.”

In 2015, Thomas commissioned a quality assurance analysis of his patients’ data which confirmed his observation. His experience compelled him to write a book to help parents navigate the decision-making process when it comes to vaccination by empowering them with the knowledge needed to make their own choices.

Thomas’ book, published in 2016, proposed an individualized approach to vaccination. He says he knew then that he was risking his medical career because the book “takes on the CDC’s schedule” and “the CDC’s schedule is sacred.”

The vaccinated vs. unvaccinated study

The first accusation from the Oregon Medical Board came in 2018, and additional letters of complaint followed. Having been asked to produce peer-reviewed evidence to support his approach to vaccination, Thomas hired an independent pediatrician and informatics expert to do a quality assurance project looking at health outcomes of all patients born into his practice.

That was an important inclusion criterion. As Thomas explained, “Most of the patients who come to our practice, or at least a very significant percentage of them, come because they have health problems they are worried were triggered by vaccines, and they can’t get their pediatrician, wherever they are, to slow down or stop vaccinating, so they come to the only safe place they can find.”

This meant Thomas was “getting a lot of damaged kids already,” whereas “very, very few” of those born into his practice had comparable health problems.

To include children who came to him from other practices would introduce a confounding factor that would bias the results. What he wanted to know was what kind of outcomes were resulting from various numbers of vaccinations received among patients who, from the start, were with a clinic that practices informed consent.

Thomas then obtained the approval of the state’s institutional review board to publish the de-identified data. He contrasts the approach he takes in his practice of focusing on achieving good health outcomes with the state’s myopic focus on achieving high vaccination rates.

“We shouldn’t be looking at how well somebody can follow a protocol,” Thomas said. “Monkeys can do that. We should be looking at actual health outcomes, which is what our study did.”

As he explained, “My duty is to my patients, and we have a lot of loyal patients who, you know, love the fact that we honor and provide informed consent and provide great care, and we have great outcomes, which are now documented in a published peer-reviewed study.”

As study co-author and data analyst Lyons-Weiler explained:

“This study represents a major methodological leap forward in vaccine safety studies. The results show how often vaccinating patients have to seek medical care for conditions suspected by many as potentially caused by vaccines. Our measure, the Relative Incidence of Office Visits (RIOV), is sensitive to the severity of disease and disorder — specifically, the disease burden.”

One problem with observational studies is that they are prone to selection bias. A potential bias in comparing data from vaccinated versus unvaccinated patients is the difference in healthcare-seeking behavior. The question arises, given a finding of lower rates of diagnoses among unvaccinated children, whether this is because the family’s lifestyle results in better health outcomes or because their children are underdiagnosed due to avoiding visits with the doctor.

To control for the potential confounder of differing healthcare-seeking behaviors of parents who choose not to do any vaccines, Thomas and Lyons-Weiler looked at incidence of fever and well-child visits. Because fever is a known adverse event associated with vaccination, it was expected the unvaccinated would have fewer visits for fever.

If differences in health outcomes were explainable by parents of unvaccinated children simply choosing not to go in to see their pediatrician, it would also be expected these patients would have fewer well-child visits.

As expected, they found children who received more vaccines had a higher relative incidence of office visits than children who received none. However, there was a stable trend for relative incidence of well-child visits, indicating that differences in healthcare-seeking behavior did not account for the lower incidence of fever in children who received fewer or no vaccines.

Figure 3 in the study shows the RIOV percentile for fever and will-child visits, with RIOV representing the total number of billed office visits per condition per group, which reflects the total disease burden in that study population.

Another confounding factor they accounted for was the relationship between the number of vaccines received and age. Naturally, older children would tend to have had more vaccines than younger children. To avoid comparing vaccinated children with long-term care in Thomas’s practice and unvaccinated children with short-term care, they matched patients between the two groups according to “days of care” in the practice. Because all patients were born into the practice, this correlated with age.

Matching patients to days of care also served to further protect against finding different health outcomes due to different healthcare-seeking behavior.

It is difficult to see how the findings of their study could be attributed to differences in healthcare-seeking behavior or lifestyle choices separate from the parental choice not to vaccinate. As Lyons-Weiler and Thomas remark, if their findings are explainable by different lifestyle choices, “then it would be objective to conclude that everyone should adopt the lifestyle followed by the unvaccinated if they want healthier children. That lifestyle choice includes, for many families, avoiding some or all vaccines, and thus, the lifestyle choice concern is inextricably linked to vaccine exposure.”

As they summarized their findings, “We could detect no widespread negative health effects in the unvaccinated other than the rare but significant vaccine-targeted diagnoses. We can conclude the unvaccinated children in this practice are not, overall, less healthy than the vaccinated and indeed, the vaccinated children appear to be significantly less healthy than the unvaccinated.”


The Oregon Medical Board, myopically focused on the policy goal of achieving high vaccine uptake in pediatric practices across the state, challenged Thomas to produce peer-reviewed evidence to support his approach to vaccinations.

Presumably, the board assumed this would pose an insurmountable obstacle. Yet Thomas rose to the challenge and published the data indicating his unvaccinated patients were the healthiest children in his practice.

The board, rather than taking this requested study into consideration, ignored the evidence and held an emergency meeting just days after the study’s publication during which board members opted to suspend Thomas’ license on the false pretext his approach to vaccination represented a threat to public health.

To support that charge, the board accused Thomas of “bullying” patients into accepting the alternative outlined in his book, “Vaccine-Friendly Plan.” But this, too, is a demonstrably false pretext intended to obfuscate the true reason for suspending his license, which is that the board is intolerant of doctors approaching vaccination on the principles of individualized care and respect for the right to informed consent.

Contrary to the board’s accusations, the health outcomes that Dr. Thomas has achieved with the children in his practice are enviable and should serve as a model for pediatricians across the country. The threat that Dr. Thomas posed was not to public health but to the policy goal of achieving high vaccination rates. His suspension was transparently intended to send the message to other pediatricians that if they practice informed consent, they, too, will risk having their license suspended. The message is that pediatricians must bully parents into vaccinating according to the CDC’s schedule or risk their medical career.

The true threat to public health is coming from those who willfully ignore the scientific evidence and advocate the use of coercion to achieve the policy goal. It is those who cling to this myopic and unscientific approach, grounded in rejection of the need for an individualized risk-benefit analysis and rejection of the right to informed consent, who are the true bullies and pose the true threat to both our children’s health and our precious liberty.

This article is a summary adaptation of the author’s detailed report on the Oregon Medical Board’s suspension of Dr. Paul Thomas. Click here to read the full story.


© June 2021 Children’s Health Defense, Inc. This work is reproduced and distributed with the permission of Children’s Health Defense, Inc. Want to learn more from Children’s Health Defense? Sign up for free news and updates from Robert F. Kennedy, Jr. and the Children’s Health Defense. Your donation will help to support us in our efforts.

 Connect with Children’s Health Defense