BACKGROUND Topical glyceryl trinitrate (GTN) has gained popularity as a treatment for anal fissure in the West. In our country, lignocaine is still the current treatment for the entity. This study was done to compare the effect of GTN with lignocaine in terms of healing rate and recurrence in South Asian population. METHODS A prospective, double blinded, randomised controlled trial was conducted on 50 patients (both treatment arms included) of all ages and either gender with a clinical diagnosis of anal fissure. Group A was given 0.2% GTN ointment and Group B was given lignocaine ointment. Both subjective and objective signs of healing were assessed and adverse effects of the treatment were sought. RESULTS Symptomatic relief was earlier with GTN as compared with lignocaine. Pain relief was steady and sustained in those treated with GTN but returned to pre-treatment status within 5 weeks in patients with lignocaine. After 8 weeks of treatment, 80% of patients in Group A showed clinical signs of healing compared to 32% in Group B (p=0.001). Headache was the main side effect of GTN. At 6-month follow-up, recurrence was seen in 3/8 patients in Group B compared to 8/20 in the GTN Group (p=1). CONCLUSIONS Topical GTN has earlier and a higher rate of clinical healing of anal fissure with acceptable side effects. The recurrence rate is high and comparable to lignocaine ointment. It is a safe and an effective treatment of anal fissure in a South Asian population.