Pharmaceutical companies fund the bulk of clinical research that is carried out on medications. Poor outcomes from these studies can have negative effects on sales of medicines. Previous research has shown that company funded research is much more likely to yield positive outcomes than research with any other sponsorship. The aim of this article is to investigate the possible ways in which bias can be introduced into research outcomes by drawing on concrete examples from the published literature. Poorer methodology in industry-funded research is not likely to account for the biases seen. Biases are introduced through a variety of measures including the choice of comparator agents, multiple publication of positive trials and non-publication of negative trials, reinterpreting data submitted to regulatory agencies, discordance between results and conclusions, conflict-of-interest leading to more positive conclusions, ghostwriting and the use of "seeding" trials. Thus far, efforts to contain bias have largely focused on more stringent rules regarding conflict-of-interest (COI) and clinical trial registries. There is no evidence that any measures that have been taken so far have stopped the biasing of clinical research and it's not clear that they have even slowed down the process. Economic theory predicts that firms will try to bias the evidence base wherever its benefits exceed its costs. The examples given here confirm what theory predicts. What will be needed to curb and ultimately stop the bias that we have seen is a paradigm change in the way that we treat the relationship between pharmaceutical companies and the conduct and reporting of clinical trials.