However, labels for generic drugs must include the same warnings and precautions as the branded product. AstraZeneca initially filed a citizens' petition requesting that the FDA not approve any generic that omits this safety data from their label. When the FDA denied the petition, AstraZeneca filed suit against the FDA. However, the suit was dismissed by the court and generic Seroquel was approved on schedule. However, AstraZeneca did manage to win a separate battle to protect Seroquel XR, the long-acting formulation, as the drug's patent was found valid and protected until 2017.

Overall, pharmaceutical companies and the FDA usually maintain a rather positive relationship, with newsworthy disputes occurring relatively rarely. While drug companies will naturally tend to disagree when the FDA rejects their marketing applications or request additional data before approving, the agency must act first to protect the public.

Likewise, drug developers do not wish to introduce a harmful product in the market, the result of which would only tarnish their reputation and lose the confidence of their customers. A recent case of a rejection turning out to be quite prescient was the initial rejection of Merck's marketing application for Tredaptive, a drug for treating low high-density lipoprotein (HDL) cholesterol. Although the drug was already approved in Europe and some other countries, the FDA wanted to know if Tredaptive not only raised HDL cholesterol (the "good" cholesterol), but also if it would actually help to prevent heart attacks, which is the ultimate purpose of treating dyslipidemia.

The only way to determine this is by conducting a cardiovascular outcomes trial in which tens of thousands of patients at high risk of a heart attack are followed until enough subjects experience a cardiovascular event to know if the drug had an effect or not. Upon completing such a trial, the investigators found that the drug not only had no effect on preventing heart attacks, but was also associated with increased safety risks. This news prompted Merck to pull the drug from other markets where it was approved since the benefit no longer outweighs the risk, and the European Medicines Agency (EMA) is now reconsidering their position.

From the pharma industry's perspective, dealing with the FDA is generally challenging, to say the least. The most successful companies will employ or contract executives with skill and experience in negotiating with the FDA throughout the approval process. The FDA encourages the industry to initiate communication early in the development process and maintain a relationship throughout to evade potentially avoidable pitfalls down the road.