AIM To compare the impact of laparoscopic Roux-en-Y gastric bypass (LRYGB) and laparoscopic sleeve gastrectomy (LSG) on weight loss and obesity related comorbidities over two year follow-up via case control study design. METHODS Forty patients undergoing LRYGB, who completed their two year follow-up were matched with 40 patients undergoing LSG for age, gender, body mass index and presence of type 2 diabetes mellitus (T2DM). Data of these patients was retrospectively reviewed to compare the outcome in terms of weight loss and improvement in comorbidities, i.e., T2DM, hypertension (HTN), obstructive sleep apnea syndrome (OSAS), hypothyroidism and gastroesophageal reflux disease (GERD). RESULTS Percentage excess weight loss (EWL%) was similar in LRYGB and LSG groups at one year follow-up (70.5% vs 66.5%, P = 0.36) while it was significantly greater for LRYGB group after two years as compared to LSG group (76.5% vs 67.9%, P = 0.04). The complication rate after LRYGB and LSG was similar (10% vs 7.5%, p = 0.99). The median duration of T2DM and mean number of oral hypoglycemic agents were higher in LRYGB group than LSG group (7 years vs 5 years and 2.2 vs 1.8 respectively, P < 0.05). Both LRYGB and LSG had significant but similar improvement in T2DM, HTN, OSAS and hypothyroidism. However, GERD resolved in all patients undergoing LRYGB while it resolved in only 50% cases with LSG. Eight point three percent patients developed new-onset GERD after LSG. CONCLUSION LRYGB has better outcomes in terms of weight loss two years after surgery as compared to LSG. The impact of LRYGB and LSG on T2DM, HTN, OSAS and hypothyroidism is similar. However, LRYGB has significant resolution of GERD as compared to LSG.