Background/aim: The aim of this study was to evaluate patients with inflammatory bowel disease (IBD) treated with azathioprine (AZA) and followed-up in our clinic to adverse effects. Materials and methods: We analyzed patients with IBD who were treated with AZA between April 1998 and April 2008 for adverse events. Results: Four hundred and seventeen patients that included 211 (50.6%) females (age, 38.63 ± 13.32 years) were evaluated. Two hundred and forty-two patients (58%) had ulcerative colitis, 159 (38.1%) patients had Crohn’s disease and 16 (3.8%) patients had undetermined colitis. Mean follow-up period was 42.5 ± 46 months (range, 6-288 months). One hundred and eighty-nine (45.3%) patients used AZA (66% in Crohn’s disease group, 32% in ulcerative colitis group). Mean AZA treatment period was 33.8 ± 32 months (range, 6-160 months). Discontinuing rate was 19.6% (37 cases). Causes of discontinuing AZA were as follows: Adverse events in 15 patients (bone marrow suppression in three, pancreatitis in two, hepatotoxicity in two, related malignancy in three and other events in five patients), inefficacy in 12 patients, postoperation in five patients and other causes in five patients. Major toxicity was seen in seven of 189 patients (3.7%). Conclusion: Half of IBD patients were using AZA and major toxicity and malignancy development rates during AZA treatment were low. AZA is a safe immunosuppressive agent in IBD patients.