The hidden effects of vaccines

Top vaccine researcher discusses the long-ignored harms of vaccines, calling for a complete overhaul of global vaccination policies.

A recent commentary published in the journal Vaccine by Christine Stabell Benn, of the Bandim Health Project, at the University of Southern Denmark, challenges the conventional view of vaccines.

While vaccines are recognised for their ability to prevent specific diseases, Benn highlights a critical but overlooked phenomenon: non-specific effects (NSEs).

NSEs can either bolster or weaken overall health by shaping the immune system’s response to other infections.

Dr Christine Stabell Benn, Bandim Health Project, at the University of Southern Denmark

The measles vaccine paradox

One of the earliest clues about NSEs emerged in the 1990s with the high-titre measles vaccine (HTMV).

Designed to immunise infants as young as three to four months, the vaccine protected against measles but had another devastating effect—it doubled the overall mortality rate in girls.

This alarming discovery led to the World Health Organization (WHO) to pull the vaccine in 1992, revealing that even effective vaccines can have unintended, sex-specific harms.

The BCG vaccine: Protection beyond tuberculosis?

Conversely, the Bacillus Calmette-Guérin (BCG) vaccine, primarily used to prevent tuberculosis, appears to have protective effects beyond TB.

Studies in Guinea-Bissau and Uganda found that administering BCG at birth reduced infant mortality and morbidity by 29% to 38%—far beyond what could be explained by TB prevention alone.

Could the vaccine stimulate the immune system in a way that helps fight off various infections?

During the Covid-19 pandemic, some studies even suggested that BCG vaccination reduced infection risk in vulnerable groups and may have reduced all-cause mortality across all trials, reinforcing its broad protective benefits.

The dark side of non-live vaccines

“Live vaccines” which contain an attenuated form of the live pathogen—such as BCG, oral polio, and measles (standard-titre) —have been linked to reduced mortality, suggesting they save far more lives than expected through positive immune training.

However, “non-live vaccines” exhibit worrying patterns.

Three doses of diphtheria-tetanus-whole cell pertussis (DTP) vaccine have been the backbone of immunisation programmes in low-income countries.

Research by Benn and colleagues found that DTP-vaccinated children had higher mortality than DTP-unvaccinated children.

In the figure below, all studies uniformly suggest that being DTP-vaccinated is associated with higher mortality than not being DTP vaccinated.

Source: doi:10.1016/S1473-3099(19)30742-X

Overall, DTP vaccine is associated with a 2-fold increase in mortality, and this deleterious effect of DTP was particularly pronounced for females.

Similar concerns have emerged for other non-live vaccines.

Specifically, a higher female-male mortality ratio among vaccinated children has been observed for five others: the pentavalent vaccine, hepatitis B vaccine, H1N1 influenza vaccine, RTS,S malaria vaccine, and inactivated polio vaccine.

These findings suggest that the type of vaccine—not just the disease it targets—matters for overall health outcomes.

Why hasn’t policy caught up?

Despite strong evidence, NSEs are largely ignored in vaccine policy. The WHO acknowledged in 2014 that some vaccines reduce all-cause mortality, while others may increase it, yet nothing changed.

One challenge of observational studies is the "healthy vaccinee bias"—healthier children are more likely to be vaccinated, skewing the results towards benefits of any vaccine.

But Benn argues that randomised trials, wherever conducted, have largely confirmed NSEs, making the risks harder to dismiss.

"We must rewrite our understanding of vaccines," writes Benn. "It is no longer tenable to maintain a narrow perspective on vaccines as biological preparations that induce specific protection against a specific disease.”

The latest edition of Plotkin’s Vaccines, the world’s leading textbook on vaccines, includes a dedicated chapter on non-specific effects and unequivocally states that "it is clear that vaccines have NSE."

Yet, these effects remain overlooked in vaccine policy.

We need smarter vaccine policies

Benn stresses the need for tailored policies rather than a one-size-fits-all approach:

• BCG strain matters: The BCG-Russia strain failed to lower mortality in India, while the BCG-Denmark strain did.

• Vaccine order matters: DTP's risks were highest when given last; a live vaccine afterward reduced harm.

• Covid-19 vaccines were not assessed for all-cause mortality: Phase 3 trials suggested adenovirus-vectored vaccines may have broader immune benefits, while mRNA vaccines showed no overall mortality advantage.

"NSEs make life more complicated for policymakers and regulators," Benn acknowledged.

"However, the reward is the auspicious prospect of wiser vaccination programs designed to protect against specific diseases and provide general immune training with even bigger benefits."

Benn proposes several actionable steps, such as redefining BCG vaccination from a tuberculosis-specific intervention to a tool for reducing neonatal mortality, as well as ensuring live and non-live vaccines are given in the safest, most effective order.

Ultimately, she argues that policy should prioritise all-cause mortality studies—so future vaccine trials measure overall health impacts, not just disease-specific protection.

A shift in the vaccine debate?

The discussion around vaccine policies is particularly relevant now, with Robert F. Kennedy Jr. at the helm of the U.S. Department of Health and Human Services (HHS).

Feb 2025: Robert F. Kennedy Jr sworn in as secretary of Health and Human Services

Kennedy has long been an outspoken critic of the lack of transparency in vaccine safety discussions, and his leadership could signal a shift toward more scrutiny and potential reform in vaccination policies.

Whether this will lead to meaningful policy changes remains to be seen, but it certainly opens the door for a much-needed discourse on vaccine science beyond the rigid mantra of "safe and effective."

No drug that is effective can be totally safe; there will always be harms and it is essential to understand them.

At Kennedy’s confirmation hearings, we saw a stark example of "vaccine absolutism"—the refusal to entertain any discussion of nuance in vaccine policy.

Ironically, those most fearful that Kennedy will roll back vaccinations are, in their efforts to suppress debate and control the narrative, causing more damage to public confidence in vaccines.

As one of my colleagues always says, “If you have nothing to hide, then hide nothing.”

If we want to restore trust in vaccination, we must move beyond the binary thinking of "pro-vaccine" versus "anti-vaccine" and instead foster a more open, evidence-based discussion about their benefits and harms.

Acknowledging the complexity of vaccines—both their intended and unintended effects, positive and negative—is the only way to ensure public health policies truly serve the best interests of all.

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