The National Institutes of Health (NIH), the leading public funder of biomedical research globally, boasts an impressive legacy. Its support has been pivotal to earning over 100 Nobel Prizes and has contributed to the approval of more than 99% of drugs authorized by federal regulators between 2010 and 2019.

It’s little wonder the NIH is often referred to as “the crown jewel of the federal government.” However, as President-elect Donald J. Trump and the Republican-led Congress prepare to take office, the agency’s future hangs in the balance.

The incoming Secretary of Health and Human Services, Robert F. Kennedy Jr., who will oversee the NIH, is a vocal critic of federal scientists and has a history of spreading misinformation about vaccine safety. He has suggested diverting the agency’s focus away from infectious disease research toward chronic illnesses.

Meanwhile, Dr. Jay Bhattacharya, Trump’s choice for NIH director, is a Stanford professor known for his controversial stance during the pandemic. He advocated for allowing the coronavirus to spread among healthy individuals to achieve herd immunity, a theory widely criticized as unscientific and unsafe. Dr. Bhattacharya has called for major restructuring of the NIH, claiming it is controlled by “small-minded bureaucrats” who hinder innovation.

While even proponents of the NIH acknowledge the need for modernization, experts argue that the drastic changes proposed would face significant legal hurdles and require strong congressional backing.

Many fear that the new administration could weaken the NIH by cutting funding for critical research, with potentially far-reaching consequences for science and public health. A Trump transition team spokesperson has stated that cabinet appointees aim to eliminate “wasteful spending” in healthcare and restore it to the “Gold Standard.”

The NIH, comprising 27 specialized institutes, employs approximately 6,000 scientists and allocates over 80% of its $47 billion budget to external researchers through a highly competitive grant process. Historically, it has enjoyed bipartisan support, with Congress often rejecting proposals to cut its budget, including an 18% reduction suggested by Trump during his first term.

However, the COVID-19 pandemic has intensified political scrutiny of the agency. Republican lawmakers have criticized its handling of the virus’s origins and its financial ties to research in Wuhan, China. Vaccine skeptics have also targeted the NIH, particularly for its involvement in developing Moderna’s COVID-19 vaccine.

Some Republican members of Congress have proposed consolidating the NIH’s 27 institutes into 15 and increasing political oversight, citing issues like research duplication and misconduct. Additionally, the Heritage Foundation’s Project 2025 suggests redirecting parts of the NIH budget to state-level scientific research.

Dr. Bhattacharya has expressed intentions to decentralize NIH leadership, arguing that current administrators stifle creativity. His association with the Great Barrington Declaration, which advocated for herd immunity during the pandemic, remains controversial and was criticized by prominent health experts, including former NIH Director Dr. Francis Collins.

Robert F. Kennedy Jr., meanwhile, has proposed reallocating half the NIH budget to alternative and holistic health approaches and replacing a significant portion of its workforce after Trump’s inauguration. His past comments have included calls to criminalize vaccine scientists, further fueling concerns about his leadership.

While sweeping reforms would face legal and congressional challenges, the new administration could still influence the NIH through budgetary decisions and the appointment of institute directors aligned with their agenda. Experts worry that these changes may compromise the agency’s long-standing contributions to scientific innovation and public health.