What a pair? Not according to the FDA. This sort of thing doesn’t happen to Merck every day, but the agency refused to accept its application to turn Pfizer’s Lipitor and Zetia, the cholesterol pill it sells with Schering-Plough, into a combination medicine, according to a filing with the US Securities and Exchange Commission (see page 46).

“The FDA has identified additional manufacturing and stability data that are needed and the Company is assessing the FDA’s response in order to determine a new timetable for filing,” Merck disclosed in a terse two-line statement in the filing, which calls the drug MK-0653C. The drugmaker submitted its filing to the FDA only last September, an unusually speedy rejection by the agency, (UPDATE: unless the decision was based on completeness as opposed to content).

“For a company this size, this is not the norm,” Steve Brozak, an analyst with WBB Securities, tells the Associated Press. He adds that the move may reflect the agency’s new-found caution and there may be relatively minor questions, “or, it could mean that they’ve found something they don’t like.”

Merck is about to acquire Schering-Plough for $41.1 billion in a deal expected to close shortly. The drugmakers sell the Vytorin cholesterol combo pill, which Zetia, and Merck’s older cholesterol drug Zocor, which reduces how much cholesterol the body produces due to family history. Lipitor works the same way as Zocor, but research shows it’s more effective at preventing heart attacks, strokes and death, the AP notes.

As The Pink Sheet reminds us, Merck has stumbled several times trying to develop cardiovascular drugs recently. In June, an adenosine A1 receptor antagonist failed a Phase III study, delaying plans to file with the FDA. And its Cordaptive drug, which includes niacin, was bounced by the FDA last year after more studies were requested, delaying a filing with the agency until 2013.

Full disclosure: Ed Silverman is an editor at The Pink Sheet