"I'm betting these companies might be worth nothing," the founder of Kynikos Associates told CNBC's "Squawk Box." "They are not even close to profitable."
He said he's been short Envision Healthcare since the middle of last year and Mednax as of this year.
Both stocks tumbled after the announcement. Nashville-based Envision, which has a market cap of $4.6 billion, was down 3 percent and Mednax skidded 4.9 percent. Both regained territory from even deeper drops during the premarket.
Chanos, known for his big bet against Enron before it collapsed in 2001, said Thursday his firm has been concerned about the "rent seekers" in the U.S. health-care system who he alleges are ripping off the system. Envision Healthcare and Mednax business models involve "deception or aggressive use of reimbursement," Chanos claimed.
The Kynikos president also mentioned UnitedHealthcare's terminated agreement with Envision Healthcare after UnitedHealthcare alleged that Envision had significantly over-billed patients for its services, particularly in emergency rooms. Envision has blamed insurance companies.
"You go the emergency room, you sprain your ankle and you get two bills — one from the hospital and a separate one from the emergency room," Chanos said. UnitedHealthcare created a website targeting the company's billing practices.
Separately, the Centers for Medicare and Medicaid Services on Tuesday proposed hospitals have more transparency and publicly list their standard charges on the web. The Affordable Care Act, also known as Obamacare, mandates publishing charges, but the provision hasn't been enforced.
As for Mednax, Chanos said he doesn't like the way the company is accounting for contracts with health-care providers.
"Both companies have put themselves up for sale hoping that private equity will buy them out," he added. "Winter is coming in the U.S. health-care system."
Envision Healthcare and Mednax did not immediately respond to CNBC's requests for comment.
Kynikos Associates, with more than $2 billion in assets under management, saw its short-only fund down 12 percent last year, according to sources familiar with the matter. Kynikos' hedge fund was up 22 percent last year, sources said, adding both funds are about flat in 2018.