NIH Funding Cuts: The Shadow Docket, Executive Overreach, and the Fragility of Public Health

As the world’s largest public funder of biomedical research, the National Institutes of Health (NIH) is essential for advancing science, developing life-saving technologies and treatments, and promoting public health worldwide. From late February to April 2025, the NIH abruptly terminated at least $1.1 billion in research grants and cancelled ongoing projects totaling an additional $1.3 billion—specifically targeting numerous grants related to diversity, equity, and inclusion (DEI), gender identity, vaccine-hesitancy, and the COVID-19 pandemic. [1] Rather than citing scientific reasoning or providing justification for the cancellations, the agency has commonly stated in termination letters that the grant simply, “no longer effectuates the program goals or agency priorities.” [2] Under the second Trump administration, the drastic and rapid round of cuts targeting politically controversial areas of research has been described as an “ideological purge.” [3] This executive action, targeting politically sensitive research, quickly escalated into a major legal challenge. The subsequent Supreme Court rulings re-shaped the precedent concerning the limits of executive authority and the role of the Administrative Procedure Act (APA), thus revealing an increasing reliance on the shadow docket to shield the administration from full judicial oversight. 

The funding cuts immediately triggered significant backlash from the scientific community and multiple members of Congress. On April 2, 2025, the American Public Health Association; Ibis Reproductive Health; the United Automobile, Aerospace, and Agricultural Implement Workers; and researchers Brittany Charlton, Katie Edwards, Peter Lurie, and Nicole Maphis filed a complaint against the Department of Health and Human Services and the National Institutes of Health in the United States District Court for the District of Massachusetts. [4] Additionally, on April 4, 2025, 16 states filed a similar suit, Commonwealth of Massachusetts v. Kennedy, seeking relief for “across-the-board delays” in reviewing new grant applications and “widespread terminations of already-issued grants.” [5]

The plaintiffs in APHA v. NIH were represented by the American Civil Liberties Union (ACLU)—including both the national office and the ACLU of Massachusetts—along with the Protect Democracy Project and the Center for Science in the Public Interest. [6] The lawsuit alleged that the NIH violated the APA by terminating grants in an “arbitrary and capricious manner,” namely by failing to analyze relevant data or provide adequate justification and by following mandates from Department of Government Efficiency (DOGE) officials rather than forming independent decisions. [7] Secondly, APHA argued that the NIH violated the Fifth Amendment’s Due Process Clause by relying on insufficiently vague language in Directives and termination notices, which they argue leads to “arbitrary and discriminatory enforcement.” [8] They also claimed that the defendants violated the constitutional principle of Separation of Powers and cited additional APA violations, including unlawful action, exceeding of statutory authority, and unreasonable delay. [9]

The district court consolidated Commonwealth of Massachusetts v. Kennedy and APHA v. NIH and issued decisions ruling that the NIH’s actions were “arbitrary and capricious,” but did not resolve the plaintiffs’ other claims. [10] The court later denied the government’s request for a stay, stressing the harm of funding delays. [11] Following the district court’s ruling, the government sought stays from the Court of Appeals for the First Circuit, which were denied, and then petitioned the Supreme Court for a stay, stating that the lower courts were “systematically ignoring” the recent Department of Education v. California decision that challenges relating to contractual obligations—like grant terminations—belong in the Court of Federal Claims. [12] The Supreme Court ultimately issued a partial stay of the district court’s rulings on August 21, 2025, allowing the government to continue with research grant terminations but leaving intact the district court’s decision that NIH action was in violation of the APA. [13] In order to recoup the terminated grant funds, the plaintiffs would need to challenge the terminations in the Court of Federal Claims, as the Supreme Court found that the district court did not have the authority to order the government to disburse the grant payments. [14]

The Supreme Court’s 5-4 ruling was split across two separate issues: whether the NIH committed a substantive APA violation and the proper jurisdiction for financial relief of the grant terminations. Justices John Roberts, Sonia Sotomayor, Elana Kagan, and Ketanji Brown Jackson voted to keep both of the district court’s rulings in place—that the NIH violated the APA and should repay the grant funds—while Justices Clarence Thomas, Samuel Alito, Neil Gorsuch, and Brett Kavanaugh voted in favor of the government on both issues. [15] Justice Amy Coney Barrett cast the deciding vote on both sides, siding with the plaintiffs on the APA violation but agreeing with the government that the district court lacked authority to order the reinstatement of the terminated funds. [16] The majority ruling relied on precedent set in California, which held that the APA allows for judicial review of agency actions but does not grant district courts authority to provide monetary relief. [17] Therefore, decisions enforcing contractual obligations, like the reinstatement of Department of Education grants in the case of California or NIH funding, fall under the jurisdiction of the Tucker Act and must be pursued in the Court of Federal Claims. [18]

In her dissent, Justice Kentanji Brown Jackson wrote that the Government’s application for a stay should have been denied in full, emphasizing that the Court’s decision deviated from standard APA review and that splitting the claim created an “ultimately ineffectual approach” that will require plaintiffs to go on a “likely futile, multivenue quest for complete relief” if they seek recovery of grant funds. [19] She warned that this mixed ruling undermines judicial oversight of federal agencies, calling the Court’s recent actions “Calvinball jurisprudence with a twist.” [20] Calvinball, the fictional game from the classic comic strip Calvin and Hobbes, has only one rule: there are no rules. Justice Jackson says, “We seem to have two: that one, and this Administration always wins.” [21] Her pointed dissent aligns with recent criticisms and systemic concerns increasingly raised by legal analysts regarding the Court’s lack of clarity, failure to apply its own precedent, and repeated rulings in President Donald Trump’s favor through use of the shadow docket.

Legal analyst Carolyn Shapiro brought up APHA v. NIH in a piece for SCOTUSblog, using the case as an example of the Court’s unclear guidance and unequal consideration of the four traditional factors for granting a stay. [22] Shapiro argued that the majority focused exclusively on the government’s irreparable harm while neglecting harm to researchers, public health, and the public interest—all essential elements under the Court’s precedent. [23] Legal Scholar Steve Vladeck noted Justice Gorsuch’s criticism of the lower courts and referred to his argument as “dangerous,” as the Supreme Court’s recent rulings are largely unexplained and do not provide clear instructions for the lower courts. [24] Vladeck argued that such criticism of the lower courts is “further enabling an increasingly loud…anti-judiciary narrative on the right” and warned that this narrative may ultimately impact the Supreme Court itself. [25]

Historically, court decisions on the shadow docket have not been treated as precedent, but Gorsuch’s accusation that lower courts are defying the California ruling serves as evidence that the Supreme Court is increasingly treating them as such. Alicia Bannon writes for the Brennan Center for Justice that the increased use of the shadow docket has allowed the Court to consistently side with the administration’s desires with no explanation, raising questions about whether or not the decisions are valid and raising concerns about the Court’s ability to check abuses of executive power. [26] As of September 10, 2025, the Trump administration had filed 25 emergency applications with the Supreme Court, and the Court decided against the president only twice. [27] Judges have disagreed on the interpretation of these shadow docket cases that typically lack legal reasoning, with some arguing that these orders definitively set precedent and others noting that decisions based on the limited briefings have “limited precedential value” and that Gorsuch’s accusation contributes to a narrative that judges behave as “partisan activists.” [28] In a piece for the International Bar Association regarding President Trump’s relationship with the judiciary, William Roberts writes that district judges have ruled against the administration in over 94% of cases, but the Supreme Court has intervened to block the lower courts the vast majority of the time. [29] Roberts argues that these recent patterns represent President Trump’s willingness to undermine the judiciary and push the limits of executive power, noting the increase in shadow docket decisions as well as signing executive orders punishing law firms and lawyers that are “viewed as political opponents.” [30]

Scientists, research organizations, and legal experts have broadly criticized the Court’s APHA v. NIH decision, warning that it threatens public health and undermines the stability of federally funded research. 484 staff scientists at the NIH have signed “the Bethesda Declaration,” a letter to Dr. Jay Bhattacharya, Director of the NIH, stating that the grant terminations will erode public trust, waste years of hard work and funding, and exclude American scientists from global collaboration. [31] They also wrote that the 15% cap on indirect costs will result in limited undergraduate research training, rescinded graduate student positions, and a general hindrance to university research. [32] The American Society for Microbiology, American Society for Biochemistry and Molecular Biology, the American Society for Cell Biology, and the Federation of American Societies for Experimental Biology released a statement in response to the Supreme Court ruling, emphasizing the harm already being caused through laboratory shutdowns, layoffs, and wasted progress and asserting that “when federal science funding is politicized, it is America’s future that pays the price.” [33] Those who criticize the Court’s decision agree that public funding is essential for the United States to continue to lead in scientific innovation, and that the ruling poses an especially serious risk to early-career scientists. 

Though the full impacts of this decision remain uncertain, various analyses highlight the potentially severe consequences for public health. A JAMA Health Forum analysis used qualitative systems modeling and a causal loop diagram to examine the funding dynamics and effects triggered by the NIH budget cuts. [34] The study found that NIH cuts restrict research and the scientific workforce, constraining industry growth and innovation, deprioritizing public health and prevention in favor of market-driven solutions, and ultimately driving up long-term health care costs as the burden of disease rises. [35] Using machine-learning analysis to estimate what recent research would have been lost if similar grant terminations had occurred 10 years ago, Nature Index found that such cuts could have led to the loss of a study finding the most effective way to identify lung cancer, among numerous other highly cited papers. [36] A similar study led by Pierre Azoulay analyzed what would have happened if the NIH budget had been 40% smaller from 1980 to 2007 and found that 331 out of 557 drug approvals in the sample had patents that cited NIH research, and 286 of these would have been at risk—including Gleevec, which turned a fatal myeloid leukemia diagnosis to one that can be managed effectively. [37]

Opposition to the NIH cuts is widespread, and very few defend slashing federally funded science. Those who argue that the cuts are at least partially justified focus on data that suggests federally funded science does not meaningfully contribute to economic growth or health improvements in the US. Terence Kealey, professor of biochemistry at the University of Buckingham, writes that US research funding was drastically increased in the 1950s and 60s, but GDP and Total Factor Productivity (TFP) growth were not stimulated as a result. [38] Kealey also acknowledges that the rate of increase in life expectancy slowed as research funding grew, but scholars often attribute this plateau to urban policy, environmental factors, and inadequate public health initiatives that prevent further reductions in mortality. [39]

The results of APHA v. NIH demonstrate how unchecked executive actions destabilize institutional stability and disrupt essential oversight systems. The Supreme Court’s decision to split the claim—upholding the APA violation while shifting financial remedy to the Court of Federal Claims—effectively limits avenues for researchers to pursue recourse for unconstitutional grant terminations, leaving federally funded research incredibly vulnerable to political pressure. This battle over biomedical research, unprecedented in scale, ultimately highlights the Court’s growing reliance on the shadow docket as a way to grant powerful legal decisions to the executive branch. When judicial oversight is procedurally eroded and the courts’ ability to check the power of the executive branch is diminished, the future of fields as vital as public health and scientific innovation face grave risk. 

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Sources

1. Complaint for Declaratory and Injunctive Relief, American Public Health Association et al. v. National Institutes of Health et al., No. 1:25-cv-10787 (D. Mass. Apr. 2, 2025).

2. Ibid.

3. Ibid 

4. Ibid.

5. Complaint for Declaratory and Injunctive Relief, Commonwealth of Massachusetts et al. v. Robert F. Kennedy, Jr. et al., No: 1:25-cv-10814 (D. Mass Apr. 4, 2025). 

6. Complaint, American Public Health Association, No. 1:25-cv-10787.

7. Ibid.

8. Ibid.

9. Ibid.

10. Application to Stay the Judgements, National Institutes of Health et al. v. American Public Health Association et al., No. 25A103 (U.S. July 24, 2025). 

11. Ibid

12. Ibid.

13. National Institutes of Health et al. v. American Public Health Association et al., 606 U.S. ___ (2025). 

14. Keith, Katie, and Andrew Twinamatsiko, “Unpacking the Supreme Court’s Decision Over NIH Funding,” Health Affairs Forefront, September 5, 2025, https://www.healthaffairs.org/content/forefront/unpacking-supreme-court-s-decision-over-nih-funding.

15. NIH v. APHA, 606 U.S. ___ (2025). 

16. Ibid.

17. Department of Education et al. v. California, et al., 604 U.S. ____ (2025).

18. Ibid. 

19. NIH v. APHA, 606 U.S. ___ (2025). 

20. Ibid.

21. Ibid.

22. Shapiro, Carolyn, “The Supreme Court fails to apply its own precedent and continues to sow confusion through its shadow docket,” SCOTUSblog, September 2, 2025, https://www.scotusblog.com/2025/09/the-supreme-court-fails-to-apply-its-own-precedent-and-continues-to-sow-confusion-through-its-shadow-docket/.

23. Ibid. 

24. Vladeck, Steve, “174. Justice Gorsuch’s Attack on Lower Courts,” One First, August 25, 2025, https://www.stevevladeck.com/p/174-justice-gorsuchs-attack-on-lower.

25. Ibid. 

26. Bannon, Alicia, “Supreme Court Must Explain Why It Keeps Ruling in Trump’s Favor,” Brennan Center for Justice, August 14, 2025, https://www.brennancenter.org/our-work/analysis-opinion/supreme-court-must-explain-why-it-keeps-ruling-trumps-favor.

27. Wolfe, Jan, and Nate Raymond, “Judges Vexed by Supreme Court ‘Shadow Docket’ Rulings in Trump Cases,” Reuters, September 10, 2025, https://www.reuters.com/legal/government/judges-vexed-by-supreme-court-shadow-docket-rulings-trump-cases-2025-09-10/.

28. Ibid.

29. Roberts, William, “Trump Versus the Judiciary,” International Bar Association, July 23, 2025, https://www.ibanet.org/Trump-versus-the-judiciary.

30. Ibid.

31. Stand up for Science, “The Bethesda Declaration: A Call for NIH and HHS Leadership to Deliver on Promises of Academic Freedom and Scientific Excellence,” June 9, 2025, https://www.standupforscience.net/bethesda-declaration?utm_source=pressrel&utm_campaign=bethesdadec.

32. Ibid.

33. American Society for Microbiology, “Response to SCOTUS Ruling on APHA v. NIH,” August 22, 2025, https://asm.org/press-releases/2025/august/statement-on-supreme-court-ruling-in-american-publ.

34. Jalali, Mohammad S., and Zeynep Hasgul, “Potential Trade-Offs of Proposed Cuts to the US National Institutes of Health,” JAMA Health Forum, July 25, 2025, https://jamanetwork.com/journals/jama-health-forum/fullarticle/2836433.

35. Ibid.

36. Nienaber, Vera, and Jack Leeming, “What Research Might Be Lost After the NIH’s Cuts? Nature Trained a Bot to Find Out,” Nature, September 24, 2025, https://www.nature.com/articles/d41586-025-02748-8.

37. Azoulay, Pierre et al., “What if NIH had been 40% Smaller?,” Science 389, no. 6767 (2025), 1303-1305, https://www.science.org/doi/10.1126/science.aeb1564.

38. Kealey, Terence, “Trump’s Cuts to Federal Science Budget Are Justified, So Why Doesn’t He Justify Them (Properly)?,” Cato at Liberty, May 2, 2025, https://www.cato.org/blog/trumps-cuts-federal-science-budget-are-justified-so-why-doesnt-he-justify-them-properly.

39. Yale School of Public Health, “Study Reveals Stark Differences in Life Expectancy Across U.S. States Over the Past Century,” April 29, 2025, https://ysph.yale.edu/news-article/study-reveals-stark-differences-in-life-expectancy-across-us-states-over-the-past-century/.