That’s what FDA commish Andy von Eschenbach is threatening in a letter sent yesterday to agency employees. As many as 2,000 could get layoff notices as early as this coming week if Congress fails to renew user fees for drugs and medical devices, the Associated Press reports.

Andy is confident that lawmakers will renew the user fees, but he also wants them to know that a consequence of not renewing the fees would be a ‘reduction-in-force’ notice. The layoffs would take effect 60 days after issuance of such a notice. “All parties fully understand the importance of meeting the September 21st deadline because no one underestimates or fails to appreciate the disruption and demoralizing impact that even the threat of a RIF is having on you and your families,” Andy wrote.

Both chambers of Congress have passed legislation that renews the Prescription Drug and User Fee Act, or PDUFA, through 2012. The bill authorizes the FDA to use industry fees to defray the cost of reviewing new meds. But the House and Senate are trying to resolve the numerous differences between their respective bills.

The real question: “Who should go, anyway?”

In the wake of the Vioxx withdrawal and subsequent problems with other drugs, lawmakers seized on the legislation to overhaul how the FDA handles the safety of the drugs it regulates. The bills gather together other legislation as well, including the reauthorization of a medical device industry user fee program.

Andy added that the FDA and congressional staff were working around the clock, including weekends to finalize the legislation. “As we approach next Friday, I will have further opportunities to update you and discuss our options and plans,” he concluded.”