INTRODUCTION Topical Glyceryl Trinitrate (GTN) has gained popularity as first line treatment for anal fissure. This study was done to investigate the role of GTN as a treatment option for both acute and chronic anal fissure in a South Asian setting. METHODS A prospective, double blinded, randomised controlled trial was conducted at a teaching hospital in Pakistan on 50 consecutive patients with either acute or chronic anal fissure. Group A (25 patients) was given 0.2% GTN ointment and Group B (25 patients) lignocaine ointment twice daily for 8 weeks. Healing was then assessed clinically and adverse effects of the treatment were sought. Patients were reviewed at 6 months for recurrence. RESULTS Symptomatic relief was earlier in Group A compared to Group B (average 8 vs 13 days). Pain relief (assessed with Visual Analogue Scale for Pain) was maintained in those treated with GTN but returned to pre-treatment scores within 5 weeks in patients with lignocaine. After 8 weeks of treatment, 77% of patients with acute and 81% with chronic anal fissure in Group A showed clinical signs of healing compared to 44% and 25% in group B (p value 0.015 and >0.001). Significantly more patients in Group A complained of headache (68% vs 28%, p=0.01), but this was always mild and no patient had to stop the treatment. At 6 months follow-up, recurrence was seen in 24% patients in Group A and 38% in Group B. All were subjected to another course of GTN and 60% of the patients responded. CONCLUSION Topical GTN is an effective treatment for both acute and chronic anal fissure. Mild headache is the most common side effect but is tolerated well. The results of this study are comparable with the published international data.