The ouster of Professor Peter Gotzsche who headed the Nordic Cochrane Centre, from Cochrane, a respected international research organisation, has provoked a crisis of confidence in the organisation's future. Disputant and bystander reactions on this issue are presented, as well as concerns regarding conflicts of interest and the reliability of Cochrane reviews. Cochrane's crisis mirrors the larger crisis of confidence that pervades the entire enterprise of medical research. We note that within weeks after Gotzsche was expelled from Cochrane, the HPV vaccine (whose Cochrane review he had publicly criticised for conflicts of interest and poor science) received a license expansion in the United States that might be worth billions of dollars to the manufacturer. Finally, we suggest a variety of new approaches that could strengthen the value of Cochrane analyses, broaden Cochrane's approach to include additional methodologies, and enhance its independence from financial interests.