Historically, Biogen (NASDAQ:BIIB) has definitely been a better stock than Gilead Sciences (NASDAQ:GILD). Whether you look at the last three, five, 10, 25 years, or even so far in 2017, Biogen has outperformed Gilead.

But for investors, the future matters a whole lot more than the past. Which of these two big biotech stocks is the better pick going forward? Here's how Biogen and Gilead Sciences compare.

Two scientists side by side in lab

Image source: Getty Images.

The case for Biogen

Biogen's success in recent years stemmed from its multiple sclerosis (MS) franchise. This franchise includes several blockbusters -- Tecfidera, Tysabri, and Biogen's interferon products Avonex and Plegridy. These four products, along with two other MS drugs, Fampyra and Zinbryta, are on track to generate revenue of around $9 billion this year.

The brightest star for Biogen right now, though, is spinal muscular atrophy (SMA) drug Spinraza. The drug, which Biogen licensed from Ionis Pharmaceuticals, should make close to $800 million in 2017 -- its first year on the market. Analysts project that peak sales for Spinraza could be in the ballpark of $2.5 billion. 

There's a real possibility that Biogen could have a game changer on its hands with experimental Alzheimer's disease drug aducanumab. The drug, which is being developed with partner Neurimmune, is currently being evaluated in two late-stage studies. Earlier-stage studies have showed potential for the aducanumab in slowing cognitive decline in Alzheimer's disease patients. Market research firm EvaluatePharma ranks aducanumab as the most valuable pipeline product in the biopharmaceutical industry. If successful, the drug could reach peak annual sales of $12 billion and perhaps higher. 

Biogen's pipeline also includes another late-stage candidate targeting Alzheimer's disease, BACE1 inhibitor E2609. This experimental drug hasn't generated the excitement that aducanumab has, though. In addition, the biotech has 10 other phase 2 pipeline candidates. 

The case for Gilead Sciences

Gilead Sciences has built two enormously successful franchises. The biotech rose to prominence with its highly effective HIV drugs. Gilead remains dominant in the HIV market, with eight products likely to top the $1 billion sales mark this year (four of which have already made over $2 billion year to date).

Gilead's hepatitis C virus (HCV) franchise has also been a big winner. HCV drugs Harvoni, Epclusa, Sovaldi, and Vosevi should generate in the neighborhood of $9 billion in sales in 2017. However, Gilead's HCV revenue has fallen significantly, primarily due to lower patient starts as many HCV patients have already been cured by Gilead's and its rivals' products. Still, however, the company's HCV franchise should continue to contribute significant cash flow for years to come.

Thanks to its recent acquisition of Kite Pharma, Gilead now stands as a leader in cancer treatment using cell therapy. The biotech won U.S. regulatory approval of CAR-T (chimeric antigen T-cell) drug Yescarta in October as a third-line treatment for certain types of large B-cell lymphoma. If approved for additional indications, Yescarta could reach peak annual sales of $2.7 billion. The ramp-up to that sales level will likely be a slow one, however.  

Gilead eagerly awaits regulatory approval for its bictegravir/F/TAF combo in treating HIV. This combo could become one of the biotech's biggest HIV drugs yet, with analysts projecting peak sales of around $5 billion. 

The company's pipeline includes seven late-stage programs and 11 phase 2 programs. Gilead's most promising assets are its experimental drugs targeting treatment of non-alcoholic steatohepatitis (NASH), particularly late-stage candidate selonsertib, and its JAK1 inhibitor filgotinib, which is being evaluated in three late-stage studies for treatment of autoimmune diseases. 

Better buy

On the surface, Biogen appears to be the better choice. Although the biotech's revenue isn't growing a lot, that's better than the huge revenue declines that Gilead is experiencing. And aducanumab just might become one of the most successful drugs ever within the next few years.

I have two major concerns with Biogen, though. One is that the pace of sales erosion for its MS franchise will probably accelerate soon. The other is that Biogen's future fortunes rest way too much on what happens with aducanumab. Drug development is always a risky business, but that's especially true for developing Alzheimer's disease treatments. Several once-promising Alzheimer's drugs have flopped in late-stage studies.

But what about Gilead's continued HCV woes? I think HCV sales will stabilize within the next couple of years. Gilead CEO John Milligan even thinks the company will have smooth sailing ahead in HCV. Combining that anticipated stabilization with great potential for the bictegravir/F/TAF combo gives Milligan enough confidence to predict that 2018 will be "the beginning of a growth phase" for Gilead. I wouldn't be surprised if he's right.

Gilead also has a huge cash stockpile of more than $40 billion (including cash, cash equivalents, and marketable securities). The company is almost certainly going to make additional acquisitions that could fuel growth over the long run. Biogen isn't in as good of a position for deals, with around $3.5 billion in cash, cash equivalents, and marketable securities. 

I suspect Biogen could be the better stock over the next year or two. Over the long run, though, I'd go with Gilead.

Keith Speights owns shares of Gilead Sciences. The Motley Fool owns shares of and recommends Gilead Sciences and Ionis Pharmaceuticals. The Motley Fool recommends Biogen. The Motley Fool has a disclosure policy.