Anal Fistula in ano is an abnormal connection between ano-rectum and the perianal skin. It is a common condition with a prevalence of 12 to 28/100,000 of population per year. There are many techniques to manage this condition. The aim of each surgery is to prevent recurrence and anal incontinence with early healing with decreased post-operative morbidity. LIFT and Fistulotomy are common types of surgery used in the management of Fistula in ano. This aim of this study is to compare the outcomes of the two procedures LIFT and Fistulotomy in cases of Intersphincteric and Low Trans-sphincteric fistulas primarily in term of healing, infection, recurrence, and anal incontinence. This prospective study was carried out in the Department of Surgery at North Delhi Municipal Corporation Medical College and Hindu Rao Hospital, Delhi between April 2017 and November 2017. A total of 50 cases were taken up and assigned either procedure randomly. Patients with recurrent fistulas, complex fistulas, high fistulas, fistulas with more than one external openings and fistulas due to secondary causes (Koch’s, Crohn’s Malignancy, post-radiation) and those with systemic diseases such as diabetes, HIV, immunosuppressive conditions were excluded. The patients were followed up for maximum 12 months studying recurrence, incontinence and post-operative morbidity. Of 50 patients 45 were males and 5 females all presenting with a history of recurrent perianal discharge. All patients underwent clinical examination, digital fistulogram, trans anal USG (12 patients) and/or MR Fistulogram to assess the characteristics of the fistula. 22 patients underwent LIFT and 28 underwent Fistulotomy. 25 patients were followed up for 3 months and rest for 2 months. There was recurrence in 4 patients (3 in LIFTand one in fistulotomy), unhealed sinus in 10 patients (7 in LIFT and 3 in fistulotomy) which required re-surgery. No patients had incontinence and 15 patients (10 –LIFT and 5- Fistulotomy) had delayed healing (4 to 6 wks).