Azathioprine is the most common drug used to maintain clinical remission in inflammatory bowel disease. This drug is also important as a steroid-sparing agent in steroid-dependent and chronically active inflammatory bowel disease. Nevertheless, many questions remain concerning the optimal treatment regimens of azathioprine. The dose of azathioprine has to be reduced or the therapy has to be discontinued frequently because of drug-induced toxicity. In this review, we discuss monitoring of thiopurines, adverse events, malignant complications and how to use azathioprine safely and usefully.