The federal government pays for most residencies through Medicare. However, the Balanced Budget Act of 1997 capped the number of residencies the federal government would fund. The alternative is asking hospitals to pay for additional residency spots on their own, which is often infeasible due to their limited budgets.
It has nothing to do with the ACA.
And since I did work in finance I can help explain the budget process.
Medicare reimbursement is set by Congress. Hospitals get a fixed amount for every diagnosis. Get them out the door early you win. And if you are a medicare provider you can only increase your rates so much per year unlike the insurers.
So it becomes a game come budget time to give away as much as you can to medicare and recoup what you give away from the insurers.
But then the insurers step in and say well if we don't get a discount on your billing we'll treat you as an out of network hospital for your patients who happen to be our customers.
Starting to get the picture of how F'ed up the whole thing is?
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