Gilead Sciences (NASDAQ:GILD) got bad news from the Food and Drug Administration this week when it learned that its inhaled antibiotic treatment to help with cystic fibrosis-related infections wouldn't be approved.

In rejecting Gilead's aztreonam lysine, the FDA requested that Gilead run another study for the compound before it would grant it marketing approval. Gilead said it would have further discussions with the FDA to see whether it could be approved without further clinical trials. That probably isn't going to happen -- no drugmaker I'm aware of has had much luck getting the FDA to change its mind about more clinical trial work. For instance, Encysive Pharmaceuticals is conducting another phase 3 trial for Thelin per the FDA's request.

Even though having to do another clinical study likely will add more than a year before aztreonam lysine can be approved, the good news is that in its press release, Gilead signaled that the FDA didn't have any problem with the drug's safety. Considering that Elan (NYSE:ELN) has long been marketing an intravenous version of the compound -- Azactam -- it doesn't surprise me that the FDA would be comfortable with aztreonam lysine's safety.

As a consolation, Gilead still has shots with the European Union and other regulatory agencies to get aztreonam lysine approved for marketing. Encysive, for example, was able to get Thelin approved overseas while still working on approval here in the States.

It's not as if getting the drug approved would make or break Gilead. Rival compounds like Azactam and Novartis' (NYSE:NVS) Tobramycin produced sales of $52 million and $91 million, respectively, in the U.S. in the first half of the year. Gilead's revenue was $4.2 billion for 2007, so FDA approval of aztreonam lysine would have added just a few percentage points at most to the company's sales next year.

HIV franchise drugs and how well they compete against rival therapies from Merck (NYSE:MRK) and GlaxoSmithKline (NYSE:GSK) will have a much larger impact on Gilead's future than aztreonam lysine would.

Even without this approval, will Gilead outperform or underperform the market? Log onto Motley Fool CAPS, the Fool's investor knowledge database, and register your call. It's fun and it's free. 

Fool contributor Brian Lawler owns no shares of any company mentioned in this article. GlaxoSmithKline is an active Income Investor pick. The Fool has an A-plus disclosure policy.