Exclusive: The fate of the CDC hinges on this new, three-page table.
Congress seems to have grown a spine. Will it hold?
We’ve got an exclusive here in Inside Medicine, thanks to our sources within HHS. Thanks for reading. Your support is what makes this work possible.
Since its earliest days, President Trump’s second administration has waged a relentless attack on the CDC. First there was mass censorship. Next there were arbitrary “reductions in force.” Both of these were Project 2025, incarnate. Then came Secretary Kennedy, whose confirmation launched another kind of attack—a sustained campaign to force experts out, only to replace them with his conflict-of-interest riddled allies from the trenches of the anti-vaccine (or otherwise scientific crank) movement. Lately, that is where our focus has been, and rightfully so.
However, the existence of the CDC at all comes down to one thing: funding. That’s an issue we may have forgotten about, thanks to competing news cycles. It’s time to return to this issue.
Remember that how much funding the CDC receives is actually (read: legally) determined neither by DOGE nor by any Office of Management and Budget executive orders, but by Congress. Therefore, the fate of a massive agency reorganization proposed earlier in the year and deep, deep cuts to established programs (read: elimination in many cases) as first reported here in Inside Medicine a few months ago, comes down to Congress. Would it fecklessly go along with the President’s budget request, which included cutting the CDC’s annual funding from $9.2 billion to $4.2 billion, a 54% reduction? Or would it locate its spine?
We just found out—at least in part. Last week, the House of Representatives released its version of the proposed appropriations for fiscal year 2026, known as its “markup.” (The Senate already did so in July). That means that, at last, we can compare what the President wants to what Congress wants. Thanks to a never-before-seen table, provided exclusively to Inside Medicine by an HHS employee on the condition of anonymity, we can now sort through it. (The authenticity of the document was verified by a separate CDC employee, as well as an assessment of document metadata, which I helpfully scrubbed from the document before posting it here).
Here’s a table of the thirteen main sections of the document, plus the totals. (If you want to know more about the specific programs within these categories, you can find the entire three-page PDF document below.) The first column shows the funding for each program for fiscal years (FY) 2024-2025 (which were identical because Congress couldn’t agree on a new bill for FY 2025, so the government was funded by a “continuing resolution,” which just replicates the previous years’ funding levels). Next comes the proposed funding level request by President Trump for FY 2026. After that, we see what the House and Senate put in their latest versions of the appropriations bill, where all this will eventually be decided
Congress says “No!” to some deep cuts Trump wanted for the CDC.
So, the short answer is that Congress now seems poised to reject many of President Trump’s most severe proposed CDC cuts. Where President Trump asked for CDC funding to be slashed by an astonishing 54% ($9.2b down to $4.2), Congress basically said nah to that. The House plan would decrease CDC funding by 19% ($7.2b), while the Senate’s plan would decrease it by just 1% (to $9.1b).
Note that for four major lines (chronic diseases, birth defects, injury prevention, and occupational health), President Trump’s budget asked for complete eliminations—that is, reductions to $0 in funding. That said, some (but not all) of the $2.7 billion in cuts to just those four large categories that were supposed to show up in Secretary Kennedy’s new “Administration for a Healthy America” (AHA). But with the new markups, Congress is now explicitly saying that it wants these programs to stay put at CDC (albeit possibly at lower levels of funding depending on who gets their way, the House or the Senate). That means that the President’s proposed major overhaul of HHS is now very much in question. Congress is not going to provide $1.1-1.4 billion in funding for chronic disease and hundreds of millions more under the umbrella of Kennedy’s new AHA. That’s exactly what’s happening. Instead of $500 million that President Trump wanted for the AHA, the House countered with just $100 million for the project. By the way, if you really want to get into the weeds on HHS overall (I have not had a chance to read through most of it), you can access the House and Senate appropriations markups here:
A familiar process is hindered.
The three-page table comparing the President’s Budget to what each chamber of Congress proposes is not a new thing. In fact, tables like this are made every year as part of the appropriations process.
Why? So that HHS (usually CDC) representatives can go to the hill to educate lawmakers on the importance of the various funded projects. Interestingly, CDC representatives cannot advocate for any increases in funding. But they can highlight programs that might be slated for cuts in order to describe what might be lost if proposed changes become the law.
There’s a certain art to this, it seems, but it’s an important process. Hearing from constituents, including within the government, is how members of Congress are able to determine what they want support or not. It’s a typical summer activity for CDC representatives to meet with Congressional staff to go over dozens of lines of funding. Why do we want to fund sepsis initiatives? Why do we fund heart disease prevention? Some of the line items speak for themselves. Others need an explanation from an informed expert. The whole thing almost sounds wholesome.
This year, however, CDC representative activity on the hill has been markedly reduced, I’m hearing. First, there was a general halt on these activities before Dr. Susan Monarez was confirmed as CDC Director. Once Dr. Monarez arrived, some of the usual activities ramped up again, though appointments with Republican staffers were more difficult to land than in the past, which is unfortunate. But with Monarez’s recent ouster, activity is apparently once again largely on hold. One source told me that no proactive briefings for Congress are planned.
Still, the fact that both chambers of Congress pushed back against President Trump’s most extreme plans to slash our nation’s top public health agency is welcome, even surprising, news.
What happens next? An expert weighs in on the weeds of “continuing resolutions.”
At this stage, the House and Senate have to negotiate a compromise between the funding levels in the respective markup documents. (Again, it would be nice if CDC representatives could participate in this.) If such a compromise can be reached, then the 2026 fiscal year appropriations process will be complete. If not, however, the government could do what it did last year, funding itself via a continuing resolution (CR). That is, the appropriations that President Biden signed for 2024-2025 will once again be used for 2026.
I asked a former HHS budget official what might happen if we just end up with another CR. He told me that President Trump’s Office of Management and Budget (OMB) would likely view the House figures as the “ceiling” for spending. “They would then release the money to the agency based on that assumption, which means programs defunded like tobacco, many injury prevention programs, global immunization, etc., would not have operating funds,” he said.
That left me confused as to how the House mark could be the ceiling if the previous appropriations bill had a higher figure? (I was told that this was a good question.)
“Unlike an actual appropriations bill, a short-term CR generally does not specify individual agency amounts. It just says the agencies (with some exceptions) can operate at, ‘the current rate of operations’, which is a level with some wiggle room for OMB to decide. Typically in short-term CRs it is based on the lesser of the following levels:
The amount the activity was appropriated in the prior year, or;
The lowest Congressional mark to date.
Part of the reason for looking at the lowest mark is generally that would be the floor of funding for a particular agency in a (successfully passed) full year appropriations bill. Sometimes the levels are negotiated up, but sometimes they stay at the floor. So, the most conservative way of calculating that rate of operations is to assume the lowest level will prevail, and then if the final level is actually higher, OMB can dole out more money for those activities and the agency is better able to plan for the remainder of the fiscal year. That is why these short-term CRs are generally bad for agencies. They essentially put any new projects, initiatives, etc on hold until there is clarity on the final levels.”
That said, this may not apply to the expected very short-term CR that will temporarily fund the government while this all gets hashed out (or not).
“I just read through the CR and it seems to direct OMB to spend at the current FY 2025 rate of operations, without leaving any ambiguity,” the former HHS employee said. That’s unexpected. The implication is that funding for programs, projects, or activities should continue at 2025 levels. “The question will be whether OMB cares or not.”
But if OMB goes rogue—which has happened this year—it could try to only provide agencies with the bare minimums needed “to keep the lights on” and to pay salaries and benefits, without actually dispensing enough money for these programs to function.
If that sounds destructive, it is. It’s also been OMB’s playbook all year. However, with both chambers of Congress saying they disagree with the President’s draconian cuts, it would be nearly impossible for that action to stand.
Closing thoughts…
To be sure, both versions of this appropriations bill cut important projects at the CDC. But neither are anywhere as catastrophic as what President Trump’s proposed budget envisioned. So, while I never thought I’d be celebrating the idea that the CDC’s funding might only fall by 1% (Senate markup) or by 19% (House markup), here we are. In times like these, less dramatic cuts sound like a win.
So, congratulations Congress, I guess. It looks like you did your job. You stood up for many important projects that matter to the American people, including those that keep us safe.
Even better, though, would be restoring all the funding, if not adding support for some of them. When the next pandemic hits, someone (i.e. everyone) is going to ask why we weren’t as prepared as we could have been. Cuts to the CDC, whether 1% or 19%, will be one of the answers.
If you have information about any of the unfolding stories we are following, please email me or find me on Signal at InsideMedicine.88.
Thank you so much for adding so much clarity to a very confusing process.
Thank you, Dr. Faust, for laying this out so clearly. The framing is important. Congress’s pushback is not a victory, it is only less of a loss than the catastrophic cuts envisioned in the Trump budget. Even a 1% or 19% reduction weakens our public health infrastructure, and when the next crisis arrives the question will inevitably be asked why we were not better prepared. Your reporting highlights how essential it is to defend CDC programs against political sabotage.