Biogen Idec (Nasdaq: BIIB) saw revenue increase 11% and adjusted earnings per share jump almost 75%, which is all well and good, but the longer-term prospects for the company aren't nearly as impressive.

Sales of Tysabri, the multiple sclerosis drug it sells with Elan (NYSE: ELN), increased 17% over last quarter, but the number of patients using Tysabri increased 22%. That's a sign that patients are taking a break from the medication -- referred to as drug holidays -- to try to avoid progressive multifocal leukoencephalopathy, a potentially deadly brain infection. Management says the percent of patients was only in the single digits, but that could change, especially as the number of cases of PML rises. Last week, the company reported three more cases and one death from the disease.

Biogen's two other major drugs are solid workhorses. Cancer drug Rituxan and multiple sclerosis drug Avonex, which competes with Tysabri and other multiple sclerosis drugs like Teva Pharmaceuticals' (Nasdaq: TEVA) Copaxone and Rebif from Merck KGaA and Pfizer (NYSE: PFE) saw revenue increase 11% and 6% respectively. But Biogen really needs a growth driver down the line as growth of the three drugs begins to decelerate.

Unfortunately, the pipeline is in shambles. It's working on an oral multiple sclerosis drug, BG-12, but it's behind both Novartis (NYSE: NVS) and Merck KGaA. The drug was also being developed to treat rheumatoid arthritis, but Biogen announced that it was dropping the program Tuesday. The company announced that testing Avonex as a treatment for ulcerative colitis would also be discontinued. Earlier in the week, Biogen and its partner announced they were dropping development of vipadenant for Parkinson's disease. The companies have a backup drug, BIIB034, but it's further behind in the clinic.

The company's new CEO, George Scangos, who came over from development-stage drugmaker Exelixis (Nasdaq: EXEL), has experience developing a pipeline, but turning around the pipeline isn't going to happen overnight.

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