Here's something you don't see every day: Total revenue for Gilead Sciences (Nasdaq: GILD) fell in the fourth quarter. You'd have to go back to 1999 to find the last quarter where the company saw a year-over-year drop in revenue.

Blame it on the swine flu. Or lack thereof.

Gilead receives royalty income from Roche for helping develop Tamiflu. Without the swine flu to bump up sales, its royalty income came back to earth and hurt the year-over-year number.

Product sales were actually up 7% year over year. Top-selling HIV treatment Atripla -- a combination of Gilead's Truvada and Bristol-Myers Squibb's (NYSE: BMY) Sustiva -- continues at a decent-but-not-ecstatic 11% clip.

But the royalties head straight to the bottom line while product sales have cost of goods and selling expenses that have to be deducted. Adjusted earnings fell by 9.8% in the fourth quarter. Adjusted EPS ended up year over year, but that's only because Gilead's share buyback cut the share count by 11%!

An increased R&D budget also contributed to the decreased earnings. That's not so bad as long as Gilead is translating the results into new medications. GlaxoSmithKline (NYSE: GSK) and Pfizer (NYSE: PFE) aren't going to let Gilead run away with the HIV drug market.

But Gilead announced yesterday that the Food and Drug Administration had refused to accept its marketing application for the combination of Truvada and Johnson & Johnson's (NYSE: JNJ) TMC278 -- affectionately referred to as B-Tripla by investors. Gilead was missing information about proper manufacturing of the drug. The delay isn't the end of the world, but it's a little embarrassing for a company that should know how to get HIV drugs approved.

Now, Gilead can get back to growing revenue -- as long as it can get the Food and Drug Administration to sign off on its drugs.

Johnson & Johnson and Pfizer are Motley Fool Inside Value selections. Gilead Sciences is a Motley Fool Stock Advisor selection. GlaxoSmithKline is a Motley Fool Global Gains pick. Johnson & Johnson is a Motley Fool Income Investor recommendation. Motley Fool Options has recommended a diagonal call position on Johnson & Johnson. The Fool owns shares of GlaxoSmithKline and Johnson & Johnson. Motley Fool Alpha owns shares of Johnson & Johnson. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors.

Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Fool has a disclosure policy.