Azathioprine and 6-mercaptopurine represent important first-line immunosuppressive drugs in the treatment of inflammatory bowel disease. Owing to 45 years of clinical experience with thiopurines in inflammatory bowel disease, there currently exist strong data from numerous clinical trials and meta-analyses, which clearly document the therapeutic efficacy of azathioprine and 6-mercaptopurine in the treatment of inflammatory bowel disease. However, the exact molecular mechanism of action of these drugs was insufficiently understood for a long time. During the last few years, important new insights into the intracellular effects of azathioprine have been gained and thiopurines have been identified as strong inducers of T-cell apoptosis. This article aims to summarize traditional and current concepts of azathioprine-mediated effects and endeavors to discuss the resulting clinical implications.