On Friday, two major drugmakers got the wrong end of the Food and Drug Administration's wishbone for drug applications. Both plan to resubmit their applications for approval in the first half of next year, but the delays likely will have different effects on the companies.

First, the FDA sent AstraZeneca (NYSE:AZN) a complete response letter for motavizumab, its respiratory syncytial virus (RSV) prophylactic. AstraZeneca didn't say what problems the agency had with its marketing application, but it did let investors know that more clinical trials probably wouldn't be necessary.

The delay shouldn't hurt AstraZeneca much because motavizumab likely will just replace sales of Synagis, its current RSV treatment. AstraZeneca eventually needs to get the more-effective motavizumab approved to compete with up-and-coming drugs like Alnylam Pharmaceuticals' (NASDAQ:ALNY) RNAi-based treatment for RSV, but Alnylam's drug is still in phase 2 development, so AstraZeneca has some time to fix the issues cited by the FDA.

Second, Eli Lilly (NYSE:LLY) didn't wait for any letter, but instead pulled its application to expand Cymbalta's label to include the treatment of chronic pain. The company's meetings with the FDA were clearly not going well -- the agency had "questions about efficacy and dosing" -- so it'll regroup and submit the package again after adding data from a study showing that the drug treats chronic osteoarthritis pain in the knees.

Sales of Cymbalta have trounced other depression drugs like Pfizer's (NYSE:PFE) Zoloft and GlaxoSmithKline's (NYSE:GSK) Paxil in part because it also treats diabetic nerve pain and a pain disorder called fibromyalgia. If the blockbuster drug had won approval to treat chronic pain, it would have been a big boost to Lilly, and the increased sales surely will be missed.

When investors value label expansions or drugs in a company's pipeline, they need to factor in the possibility of a delay -- especially in this regulatory environment. More importantly, you've got to know how much a delay is going to hurt the company if the drug isn't approved on its first go-round.

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