Merck & Co. (MRK) and Schering-Plough Corp. (SGP) have agreed to pay $41.5 million to settle lawsuits accusing the companies of marketing their cholesterol drugs misleadingly and failing to disclose the results of a negative clinical study in a timely manner.

It's the second legal settlement in as many months related to the jointly marketed drugs, Vytorin and Zetia, but it doesn't resolve all of the outstanding litigation. A U.S. Department of Justice investigation is still pending, as are lawsuits alleging securities-law violations.

Merck has agreed to acquire Schering-Plough in a deal expected to close by the end of the year. Shareholders of both companies are scheduled to vote on the deal Friday.

The latest settlement resolves more than 140 lawsuits pending in U.S. District Court for the District of New Jersey that were seeking class-action status to represent consumers and insurers who purchased, used or paid money towards the purchase Vytorin or Zetia. Some suits alleged the drugs caused personal injuries, or sought a court order that the companies pay for medical monitoring of users of the drugs.

Vytorin is a single-pill combination of two drugs: Zetia and simvastatin. In early 2008, Merck and Schering-Plough released a study, titled "Enhance," which showed that Vytorin was no better than simvastatin alone at mitigating thickening of the arteries, despite producing a greater drop in bad cholesterol levels.

The study cast doubt on the drugs' efficacy and triggered a drop in sales of both drugs, while a subsequent study raised new safety concerns about the drugs. Merck and Schering-Plough have defended the drugs' efficacy and safety.

In addition, Merck and Schering waited nearly two years after Enhance was completed to release the results, which led to accusations that the companies purposely delayed the release because they knew the study was negative and would hurt sales. The companies have said data-quality problems with the study required repeated analyses, and that top company officials didn't know the results until shortly before they were released.

Merck and Schering didn't admit any misconduct or liability in the latest settlement. The settlement with proposed class-action suits requires court approval. A separate portion of the settlement doesn't require court approval.

Last month, the companies agreed to pay $5.4 million and comply with certain rules to settle a probe by 35 U.S. states and the District of Columbia into whether their handling of the Enhance study violated consumer-protection laws.

While Vytorin has presented a legal headache for Merck and Schering-Plough, the amounts paid so far pale in comparison to the nearly $5 billion Merck had to fork over to settle personal-injury and other litigation surrounding its former pain drug Vioxx.

Still, more and bigger Vytorin settlements could be in the works. In September 2008, Merck received a letter from the Justice Department saying it was investigating whether the companies' promotion of Vytorin caused false claims to be submitted to federal health-care programs; the companies are cooperating with the probe. The companies also have received letters from Congressional committees seeking information about their handling of the Enhance trial.

Merck's shares fell 16 cents to $29.68 in recent trading; Schering shares were off 12 cents at $26.34.

The two companies have also faced separate lawsuits over their pending $47 billion merger, which remains on track to close during the fourth quarter.

-By Peter Loftus, Dow Jones Newswires; 215-656-8289; peter.loftus@dowjones.com

(Kerry Grace Benn contributed to this article.)