In theory, our research questions should drive our choice of method. In practice, we know this is not always the case. At various stages of the research process different factors may apply to restrict the choice of research method. These filters might include a series of inter-related factors such as the political context of the research, the disciplinary affiliation of the researchers, the research setting and peer-review. We suggest that as researchers conduct research and encounter the various filters they come to know the methods that are more likely to survive the filtering process. In future projects they may favour these methods. Public health problems and research questions may increasingly be framed in the terms that can be addressed by a restricted array of methods. Innovative proposals - where new methods are applied to old problems, old methods to new areas of inquiry and high-quality interdisciplinary research - may be unlikely to survive the processes of filtering. This may skew the public health knowledge base, limiting public health action. We argue that we must begin to investigate the process of research. We need to document how and why particular methods are chosen to investigate particular sets of public health problems. This will help us understand how we know what we know in public health and help us plan how we may more appropriately draw upon a range of research methods.