BACKGROUND: The aim of this study was to compare the effect of topical glycerol trinitrate ointment (GTN) with topical diltiazem hydrochloride ointment (DTZ) in the treatment of chronic anal fissure. METHOD: Prospectively, 102 patients were treated randomly with either GTN ointment (0.2%) or DTZ ointment (2%) couple of times daily for 12 weeks. RESULTS: Forty-five patients (88.2%) in group DTZ and 36 patients (70.6%) in group GTZ had reduction of symptoms. The decrease in the symptoms for group DTZ were significantly more than that for group GTN (P= 0.02). Mean time of symptom reduction was 2.44±0.30 in group DTZ and 2.50±0.28 weeks in group GTN without significant differences between two groups (P>0.05). Complete relieving of symptoms was observed in 72.5%, 54.9% patients in groups DTZ and GTN, respectively. The frequency of complete relieving of symptoms between two groups was not significant (P>0.05). Complete remission of anal fissure was occurred in 66.7% patients in group DTZ and 54.9% patients in group GTN, which was no different, significantly. Mean time taken for fissure healing in GTN group was dramatically less than DTZ group (P=0.001). Finally, 33.3% of patients in DTZ group and 45.1% of patients in GTN group was operated. The need for operation was not significant between two groups (P>0.05). CONCLUSION: Both DTZ and GTN are equally effective and can be the preferred first-line treatment of chronic anal fissure a. However, GTN is associated with a higher rate of headache, and it should be replaced by DTZ.