Federal prosecutors have questions about how Salix Pharmaceuticals (Nasdaq: SLXP) sells and promotes its drugs, including its top-selling product Xifaxan.

The Raleigh company disclosed in a securities filing that it has received a subpoena from the U.S. Attorney’s Office for the Southern District of New York asking for documents regarding three Salix drugs: Xifaxan, Relistor and Apriso.

“The Company is in the process of responding to the subpoena and intends to cooperate fully with the subpoena and related government investigation,” Salix said in the filing. “The Company cannot predict or determine the impact of this inquiry on our financial condition or results of operations.”

Salix Vice President of Investor Relations Michael Freeman told WRAL Tech Wire that the company had no comment beyond what was stated in the filing.

A search of federal court documents yielded no legal claims in New York citing Salix. Ellen Davis, chief public information officer for the U.S. Attorney’s Office for New York’s Southern District, said that the office does not comment on its investigations.

The only federal court filing citing Salix is a Maryland lawsuit filed on Jan. 8 regarding Salix’s OsmoPrep tablets. The prescription medication purges the bowels and is used by patients preparing for procedures such as colonoscopies.

Plaintiff Kathleen Benton developed renal failure and eventually needed a kidney transplant, an outcome the suit attributes to Salix’s OsmoPrep tablets that Benton took in 2010. Benton’s suit claims Salix was aware of safety risks associated with the drug. The suit says that despite awareness that dates to 2006, Salix manufactured and marketed OsmoPrep and failed to properly notify Benton or her doctor about the risks.

Nonetheless, OsmoPrep warnings are out there. The product’s package has carried a “black box” warning – the FDA’s strictest alert – since 2009 after the agency concluded that higher health risks associated with the drug required a stronger warning of potential danger.

Salix specializes in drugs that treat gastrointestinal ailments. Xifaxan, the company’s top drug, is an antibiotic with a broad spectrum of activity against a variety of pathogens. The drug first received FDA approval in 2004 to treat traveler’s diarrhea and in 2010 its use was expanded to hepatic encephalopathy, a brain disorder associated with severe liver disease. Salix has been trying to add even more indications for the drug; an attempt to secure approval for irritable bowel syndrome was rejected by the FDA in 2011 and the company is currently conducting more clinical studies in hopes of resubmitting a drug application.

Xifaxan generated $367.4 million in revenue through the first nine months of 2012, a 38 percent increase compared with the same period in 2011. That drug alone accounts for nearly 70 percent of the company’s $537 million in sales through the third quarter.

The other drugs that New York prosecutors are interested in learning about, Apriso and Relistor, make up a much smaller part of Salix’s overall revenue. Salix’s filings don’t break out individual sales figures for those products. Apriso treats ulcerative colitis. Relistor treats opioid-induced constipation.

Salix is scheduled to release fourth quarter and full-year 2012 financial results on Feb. 28.

Salix shares closed down slightly Thursday at $48.77, a decline of 19 cents.