The present study aims to evaluate and compare the efficacy of two nitrate gels, containing isosorbide-5-mononitrate (ISMN) or glyceryl trinitrate (GTN), in the therapy of chronic anal fissure. The patients were randomly assigned to three groups: 0.1% ISMN gel (21 patients), 0.1% GTN gel (21 patients) and a placebo group (ten patients). The ethic committee of our hospital approved the protocol and informed consent was obtained from all participants. All patients underwent clinical examination, visual inspection of the fissure and anal manometry prior to and after therapy. The chronic anal fissure was completely healed in 71% of the patients treated with ISMN, 67% with GTN and in 30% from the placebo group. One patient in the ISMN group reported mild headache. Three patients in the GTN group had anal burning. Both topical nitrate treatments (ISMN and GTN) were effective for chronic anal fissures. The reduction of the anal pressure was slightly higher after ISMN treatment (28%) than the treatment with GTN (23%). However, the statistical difference was not significant (p>0.05).