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The aim of this study is to evaluate the early and late complications of laparoscopic gastric bypass (GBP) with manual versus stapled gastrojejunal anastomosis. Eighty-two patients with morbid obesity and body mass index (35–56 kg/m2) who underwent GBP were divided into two groups: manual gastrojejunal anastomosis (Group 1) and stapled anastomosis (Group 2). Early and late complications were evaluated. No differences were found between both groups in age, sex, body mass index, American Society of Anesthesia classification, and comorbidity. The mean operative time was 184.8 minutes [standard deviation (SD) = 61]; 203.5 minutes (SD = 51.9) in Group 1 and 167.4 minutes (SD = 64.2) in Group 2 (P = 0.001). The average length of stay was 5.9 days (SD = 3.9) in Group 1 and 5 days (SD = 2.1) in Group 2 (P = 0.039). Early complications were recorded in 9.7 per cent of the cases, without any differences between the two groups: 12.2 per cent in Group 1 and 7.3 per cent in Group 2 (P > 0.05). Late complication rate was 8.5 per cent, significantly higher in Group 1 (14.6%) than in Group 2 (2.4%; P < 0.05). However, in the logistic regression analysis these differences were not statistically significant (OR 0.48; 95% CI 0.03–8.37; P = 0.61). In our series, the GBP with stapled gastrojejunal anastomosis has shown lower hospital length of stay and operative time than the hand-sewn anastomosis. We have not found significant differences between both groups in early complications or in the need for reoperation. Fewer late complications were found in the group of stapled anastomosis; however, this has not been confirmed in the logistic regression analysis.