We sought to understand how knowledge about resilience is produced. We examined empirical research into resilience from the social and natural sciences, randomly selected a sample of these studies and analysed their methods using common criteria to enable comparison. We found that studies of resilience from social scientists largely focus on the response of individuals to human-induced change events, while those from natural scientists largely focus on the response of ecological communities and populations to both environmental and human-induced change events. Most studies were of change over short time periods and focused on small spatial scales. Social science studies were dominated by one-off surveys, whereas natural science studies used a diversity of study designs to draw inferences about cause-and-effect. Whilst these differences typically reflect epistemological and methodological traditions, they also imply quite different understandings of resilience. We suggest that there are significant methodological barriers to producing empirical evidence about interactions between complex social and ecological systems.