The technique of choice for gastrojejunostomy (GJ) during laparoscopic Roux-en-Y gastric bypass (LRYGB) for morbid obesity is controversial. We performed a meta-analysis comparing linear versus circular stapler technique to evaluate this issue. A systematic literature search was performed. Primary outcomes were gastrojejunal leak and stricture. Secondary outcomes were operative time, length of hospital stay, post-operative bleeding, wound infection, marginal ulcers and estimated weight loss. Eight studies involving 1,321 patients were retrieved and included in the present study. A significantly decreased risk of GJ stricture was observed after using linear versus circular stapler (RR, 0.34; 95% CI, 0.12-0.93; p = 0.04). Wound infection risk (RR, 0.38; 95% CI, 0.22-0.67; p = 0.0008) and operative time (MD, -24.18; 95% CI, -35.31, -13.05; p < 0.0001) were significantly reduced by using linear stapling. No significant differences were observed in the other outcome end-points. The use of the linear stapler compared with circular stapler for GJ during LRYGB for morbid obesity may be associated with a reduced risk of anastomosis stricture and wound infection, as well as with a shorter operative time.