Background Laparoscopic sleeve gastrectomy (SG) has surpassed Roux-en-Y gastric bypass (RYGB) as the most prevalent bariatric procedure worldwide. While RYGB and SG demonstrate equivalent short-term weight loss, long-term weight loss tends to be greater after RYGB. Differences in the effect of these procedures on gastrointestinal hormones that regulate energy homeostasis are felt to partially underlie differences in outcomes. The objective of this study was to prospectively quantify blood levels of gut hormones of energy and glucose homeostasis at one year follow up to delineate possible reasons for greater efficacy of RYGB over SG in achieving weight loss. Methods Patients undergoing SG (n = 19) and RYGB (n = 40) were studied before surgery and at 2,12, 26, and 52 weeks postoperatively. Blood samples drawn in the fasted state and after a liquid mixed meal were assayed at baseline, 26, and 52 weeks for peptide YY (PYY), glucagon-like peptide-1 (GLP-1), ghrelin, insulin, glucose, and leptin. Fasting and postprandial appetitive sensations were assessed by visual analog scale. Results At 1 year there was greater weight loss in RYGB compared with SG patients (30% vs 27%; P = 0.03). Area under the curve (AUC) after the mixed meal for PYY was greater in RYGB patients (P<0.001). RYGB patients had significant increases in GLP-1 AUC compared to baseline (P = 0.002). Ghrelin levels decreased only after SG compared to baseline (P<0.001) but were not significantly different from RYGB. There was a trend toward decreased sweet cravings in RYGB patients (P = 0.056). Conclusions Differences in gastrointestinal hormones that regulate energy and glucose homeostasis are a possible mechanism for greater efficacy of RYGB compared to SG.