This study explores the evidence-based background for treating chronic anal fissure with topically applied nitroglycerin (NTG): in part the general effect of NTG and in part how its effect compares to that of surgery, which has been claimed to have long-term complications like incontinence for flatus and faeces. Ten randomised clinical trials published up to July 2001 were retrieved. In five of six studies, NTG had an effect on healing that was better than that of placebo or lignocaine. Headache is a common side effect of the treatment. Lateral internal sphincterotomy, the operation of choice for chronic anal fissure, and topical NTG were compared in four trials. Surgery had a better healing rate, but more late complications. The results suggest that in 31-65% of patients an operation could be avoided with NTG therapy. Topically applied 0.2% nitroglycerin three times a day for four weeks is therefore the primary choice in the treatment of anal fissures. But the possibility still remains that the observed effect of NTG may be the outcome of publication bias.