Late last year, Alnylam Pharmaceuticals, Inc. (NASDAQ:ALNY) took a big hit when the company scuttled an important development program because of safety concerns. Meanwhile, plenty of clinical-stage programs at Biomarin Pharmaceutical Inc. (NASDAQ:BMRN) have been chugging along without much drama, but the stock is looking mighty expensive lately.

Both companies are developing drugs to treat rare diseases, but their similarities don't go much further. Let's see how these two biotech stocks stack up to each other to figure out which one is the better pick today.

Investor weighing a difficult decision

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Arguments for Alnylam Pharmaceuticals, Inc.

This clinical-stage biotech has a proprietary technology that uses RNA interference to silence troublesome genes. It's discovered quite a few new drug candidates over the years, but it hasn't carried any over the clinical- to commercial-stage threshold yet.

Alnylam's stock price was nearly cut in half last October after safety concerns led it to end development of a lead candidate, revusiran, which was being studied as a treatment for heart damage caused by mutated transthyretin, a protein that transports a thyroid hormone and vitamin A around the body.

A related candidate for the prevention of nerve damage, patisiran, is still winding its way through late-stage trials. With a bit of luck, its safety profile might hold up better than revusiran's and allow Alnylam to submit its first new drug application to the FDA. If successfully commercialized by Alnylam's partner, Sanofi, yearly patisiran sales could top out around $750 million, triggering milestone and royalty payments from the French pharma.

It will be easier to pin a value on patisiran once a late-stage trial with the candidate wraps up about halfway through the year, but that's not the only potential catalyst for Alnylam coming up. Early results from another Sanofi-partnered hemophilia candidate, named fitusiran, informed the design of a larger clinical trial slated to start early this year.

Soon, Alnylam expects to report mid-stage data from another experimental drug for treatment of an inherited condition that leads to super-high cholesterol. Inclisiran is under development in partnership with India's The Medicines Company, and the pair intends to begin a late-stage study around the middle of the year.

Arguments for BioMarin Pharmaceutical Inc.

Jittery investors will appreciate a key advantage BioMarin has over Alnylam. The rare-disease drug developer has a handful of commercial-stage drugs generating sales right now. When the company last reported its numbers, revenue during the first nine months of 2016 rose a sprightly 23% over the prior-year period to $816.8 million.

Despite growing its top line at an impressive rate, BioMarin's operations are still deep in the red. The company expects to post a loss of between $600 million and $630 million for 2016 when it reports full-year earnings, but a few products and clinical-stage hopefuls could push it into profitability during the years to come.

Lab researcher with a DNA double helix

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Since earning FDA approval in 2014, sales of Vimizim for the treatment of an ultra-rare metabolic deficiency known as Morquio A syndrome have taken off. Although there are perhaps just 800 children affected by the disease in the U.S., global sales of the drug are expected to total $350 million for full-year 2016.

At the moment, regulators in the U.S. and EU are mulling applications for BioMarin's Batten disease candidate, brineura. In the U.S., perhaps 1,500 patients could benefit greatly from the enzyme replacement therapy, leading to peak annual sales north of $500 million, if approved.

BioMarin's phenylketonuria drug, Kuvan, lost exclusivity in the U.S., but the company recently purchased rights to its sales in Europe, where it's protected from generic competition for a few more years. The company has a longer-lasting follow-up version of the enzyme replacement therapy on deck that significantly reduced the buildup of phenylalanine in a late-stage study. The positive results will support applications that BioMarin intends to file during the current quarter.

Running the numbers

With late-stage candidates close to the goal line and a successful history of new drug commercialization, there's a lot to like about BioMarin. Unfortunately, its recent $15.6 billion market cap is around 14.9 times trailing sales. If any unexpected events lead investors to assume profitability is further into the future, the shares have a long way to fall.

Alnylam's recent market cap of about $4 billion also includes a large slice of optimism. In its nearly 20-year history, it has yet to move a drug from clinical trials to pharmacy shelves, which means the RNA interference technology that spawned its pipeline still carries a lot of question marks.

The science behind BioMarin's candidates isn't nearly as interesting, but enzyme replacement is a generally successful approach. That's why I'm calling the bigger biotech the better buy right now.

Cory Renauer has no position in any stocks mentioned. The Motley Fool owns shares of and recommends Alnylam Pharmaceuticals. The Motley Fool recommends BioMarin Pharmaceutical. The Motley Fool has a disclosure policy.