Due to his Wall Street connections with the pharmaceutical industry, Gottlieb frequently had to recuse himself from discussions that were part of his FDA duties. He gained notoriety for calling the early termination of a multiple sclerosis drug study "an overreaction," even though three participants had died, and was highly critical of the groundbreaking Women's Health Initiative study, which found that hormone replacement therapy posed more risks than benefits to women's health.

In 2005, Eli Lilly was convicted of illegally marketing osteoporosis drug Evista for off-label treatment and prevention of heart disease and cancer. According to Justice Department documents, Eli Lilly decided to market the drug off-label when early sales of the drug for osteoporosis alone proved disappointing.

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