The purine analogues azathioprine and 6-mercaptopurine play a growing role in both inducing and sustaining the remission in patients with Crohn’s disease. They are used in a wide group of patients and often in large doses and for a long term. On the other hand, not all aspects of their multidirectional action have been definitely explored. Also, more data are being collected on increasing incidence of severe septic complications in the postoperative course of patients previously treated with purine analogues. The latter creates a threat for surgeons, who aim to regain their potential influence on the healing process and surgery effects. The article presents current literature knowledge on purine analogues’ mechanism of action, their influence on healing processes, and their potential role in induction of postoperative complications increase in patients with Crohn’s disease.