Background: Fissure in ano is one of the commonest benign and painful proctologic condition encountered in surgical practice treated by conservative line of management. Lateral sphincterotomy is the ideal treatment option for chronic refractory fissure in ano. A newer modality segmental internal sphincterotomy shows good promise in terms of early resolution of symptoms, fissure healing and prevention of anal incontinence involving division of the internal sphincter at two different levels.Methods: In comparative nonrandomized trial patients with chronic fissure in ano satisfying the inclusion and exclusion criteria were allocated to lateral sphincterotomy and segmental internal sphincterotomy groups. The outcome factors were perianal sepsis, pain relief using VAS as assessed on passing the first motion, duration of healing of fissure, assessment of incontinence using Wexner’s continence score on 30th post-operative day.Results: A total of 54 cases were enrolled, of them 31 patients underwent lateral internal sphincterotomy and 23 underwent segmental internal sphincterotomy with the mean age of patient was 34.76 years and a male to female ratio of 1.07:1. The pain score (VAS) on passing stool for the first time postoperatively was 4.5 with lateral sphincterotomy and 3.91 with segmental internal sphincterotomy which was statistically significant (P value < 0.010). The duration of postoperative healing was observed to be 27.94 days and 28.09 days in lateral sphincterotomy and segmental internal sphincterotomy group respectively. The post-operative anal incontinence was evaluated by using Wexner’s continence grading after one month which was not statistically significant between two groups.Conclusions: Segmental internal sphincterotomy could be a good surgical modality with its healing effect on fissure in ano and post-operative complications which are similar to standard lateral internal sphincterotomy.