Side effects always come back to bite a drug.

Four years ago, Dynavax Technologies' (NASDAQ:DVAX) hepatitis B vaccine Heplisav was put on clinical hold because one patient was preliminarily diagnosed with Wegener's granulomatosis. It's an uncommon inflammation of blood vessels, and it wasn't even clear if Heplisav was the cause.

The Food and Drug Administration eventually let the trial resume, and Heplisav invoked a better immune response than GlaxoSmithKline's (NYSE:GSK) hepatitis B vaccine, Engerix-B, with one less shot.

Fast forward to yesterday when an FDA advisory committee reviewed the vaccine. The panel of outside experts agreed that the vaccine produced an immune response, voting 13-1 on the question of efficacy.

On the safety front, the results were substantially different. The committee voted 8-5 that there wasn't enough safety data to approve the drug. Ruling out rare events isn't easy. Having treated more than 4,400 patients with Heplisav failed to convince doctors on the panel that the vaccine was safe.

While vaccines tend to be boring, they're still big business. Pfizer's (NYSE:PFE) Prevnar 13 racked up $868 million in sales in the third quarter. Merck (NYSE:MRK) sold $581  million worth of its HPV vaccine Gardasil in the third quarter, and its shingles vaccine Zostavax brought in $202 million. Each dose doesn't contribute that much, but the companies make up for it because nearly every patient needs to be vaccinated.

Which, of course, is the problem. The advisory panel is worried about putting the vaccine into a large number of patients without the safety profile fully characterized. Whether that's reasonable is debatable. For any drug, testing it on a larger population would make you more comfortable with the safety. No drug is perfect; at some point, you just have to say that it's good enough.

Interestingly, the briefing document from the FDA provided to the advisory panel said that the potential safety issues could be dealt with as a post-approval requirement. Shares popped on the news since it looked like Dynavax was a shoo-in for an approval. That's certainly not the case now, and the 50% drop in stock price seems warranted.

It's pretty rare for the FDA to go against its advisory panel's negative vote, but in this case I could see it happening given the FDA's stance going in. One possibility is the FDA could approve the vaccine for those with the highest risk of being infected with hepatitis B, which might make the benefit outweigh the potential for rare side effects.

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.