When Robert F. Kennedy Jr. is sworn in as the nation’s next health secretary Thursday, his first order of business will be to investigate America’s problem with chronic illnesses.

White House press secretary Karoline Leavitt told Fox News that President Donald Trump will sign an executive order creating a “Make America Health Again” commission and direct Kennedy “to investigate this chronic crisis plaguing our country and the minds and the bodies of the American people.”

What that will mean exactly remains to be seen. But here are three things to watch for as Kennedy takes the helm, based on what he and Trump have said in the past:

More study on food dyes or other food additives?

MAHA has easily emerged as a deeply popular slogan by Kennedy as much of America struggles with obesity and chronic diseases. The question though is how to do that in a way that won’t weigh down the federal budget or trigger an avalanche of legal challenges from the food and drug industry.

One possible avenue for Kennedy could be to call for additional safety studies of certain ingredients used by manufacturers, including food dyes.

Last month, the Food and Drug Administration revoked its authorization of one type of red food dye. “Red Dye No. 3” is known to cause cancer in laboratory animals but was allowed to be used by manufacturers for years because scientists didn’t believe it raised cancer risk in humans at the level typically consumed. The FDA, under President Joe Biden, acted after longtime pressure by consumer advocates.

But a different type, Red Dye No. 40, remains on the market and hasn’t been studied by the FDA in more than 20 years. FDA and health officials say there is no evidence though that it’s harmful, and food manufacturers say they need to be able to rely on ingredients generally recognized as safe.

Still, health advocates argue more can be done to look at the health impacts and or do the kind of post-market monitoring of food more common in Europe.

All of those efforts though will take significant federal resources and rely on a workforce that Trump has promised to cut.

Rewriting discrimination rules for hospitals, doctors and insurers to exclude transgender protections

Kennedy hasn’t personally focused much on the question of transgender rights. But eliminating federal rules at Health and Human Services that President Barack Obama and Joe Biden pushed to protect transgender Americans is a major priority for Trump and the conservative party.

Federal law prohibits sexual discrimination, but it’s up to the executive branch to spell out specific rules that schools, insurers and hospitals must follow if they want to retain access to federal aid.

Obama triggered a fierce legal fight in his second term when he issued federal regulations aimed at protecting transgender people from discrimination in schools and medical settings. Under rules written by Obama’s Health aand Human Services Department, doctors and hospitals were told couldn’t decline care for a person because of their gender identity. Insurance companies also were specifically prohibited from offering different benefits to certain groups, including transgender individuals and people with HIV.

Trump quickly dropped Obama’s rules in his first term, writing new rules that granted exceptions for medical providers on discrimination rules if they cited religious objections.

President Joe Biden tried to resurrect Obama’s initial rules but was swiftly challenged in court by Republican states, tossing the issue back to Trump. It’ll now be up to HHS under Kennedy, if he’s confirmed, to decide what those federal rules should say.

Making it easier for parents to send unvaccinated kids to public schools

School vaccine requirements are up to the states, and currently all 50 states have laws requiring certain vaccines for students to attend public schools.

But HHS sets the recommendations for childhood vaccines followed by schools, while the Education Department provides vital grant money to schools used to teach low-income or children with disabilities.

On the campaign trail, Trump threatened to revoke spending for schools that mandate vaccines currently recommended by public health experts and HHS.

“I will not give one penny to any school that has a vaccine mandate or a mask mandate,” Trump declared last year.

Such a move could have big implications for public health. According to the nonpartisan KFF, routine vaccination rates for kindergarten children is on the decline while exemptions are on the rise, including non-religious exemptions.

While running for president before aligning with Trump, Kennedy rejected the numerous studies finding that childhood vaccines are safe, including several studies that debunked a myth that vaccines cause autism. During his Senate confirmation, Kennedy insisted he doesn’t oppose vaccines but wants more study.

Sen. Bill Cassidy, a Republican doctor from Louisiana, said he was concerned by Kennedy’s past in “undermining confidence in vaccines with unfounded or misleading arguments.” Facing a Republican primary next year, Cassidy decided to back Trump’s pick after getting Kennedy to agree the two would work together closely.

“Ultimately, restoring trust in our public health institution is too important, and I think Mr. Kennedy can help get that done,” Cassidy said.

ABC News’ Michelle Stoddart, Molly Nagle and Kelsey Walsh contributed to this report.