Uncertainty is spreading like a cancer in the pharmaceutical investing world, and that's bad news for the segment's kingpin, Pfizer (NYSE:PFE). Still, investors should keep in mind the pharma giant's long-term prospects.

The latest pharma shocker came with Merck's (NYSE:MRK) voluntary withdrawal of Vioxx, a drug used to treat pain from arthritis. Some immediately suggested that Merck's loss was Pfizer's gain, since Pfizer's competing treatments, Celebrex and Bextra, would have a clearer field. While this may eventually be the case, for now investors just aren't buying that theory, nor are they buying Pfizer stock, which is down more than 6% today.

The pessimism seems to stem from calls from scientists for further investigation of all medicines in Vioxx's class, the so-called COX-2 inhibitors, which includes Celebrex and Bextra. According to The Associated Press, the European Medicines Agency plans to review all COX-2 inhibitors. In addition, the New England Journal of Medicine recently published an article questioning the safety of the drugs.

In the end, Celebrex and Bextra may be ruled entirely safe, but that's no consolation to investors who have to live in the here and now. It also doesn't help that the news comes on the heels of several states' approval of drug reimportation, a threat to all pharmaceutical companies' profit margins.

With all these goings-on, it's easy to see why investing in Pfizer might be considered a risky proposition in the near term. Even with the whole world seemingly crumbling around it, though, Pfizer and other pharma outfits continue to march forward with drug development efforts.

With all the resources it has at its command, Pfizer is likely to churn out more blockbusters, regardless of the outcome of the COX-2 investigations. What's more, the company is positioning itself well in the current drug pricing controversy, so it will likely have a seat at the table if any regulatory reforms of the industry are considered. For these reasons, Pfizer remains a quality choice for long-term investors.

Fool contributor Brian Gorman is a freelance writer in Chicago. He does not own shares of any companies mentioned in this article.