To examine rates of acute inpatient hospital admissions patients undergoing Roux-en-Y gastric bypass (RYGB) surgery and a matched population-based comparison cohort. Little is known about the admission rates before and after RYGB. Nationwide population-based cohort study, including all 9985 patients undergoing RYGB in Denmark during 2006 to 2010, and 247,375 matched general population comparisons. We calculated cumulative incidence of surgical complications after RYGB and incidence rate ratios (RRs) of hospital admission in RYGB patients versus comparisons before and after RYGB. Admissions for surgical complications occurred in 3.3% (n = 328) of RYGB patients <30 days after surgery and in 23.9% (n = 2367) during entire follow-up (median 4.2 yrs). Fifteen percent (n = 1486) were admitted with abdominal pain, 5.2% (n = 518) with intestinal obstruction during follow-up. Overall admission rates in RYGB patients versus comparisons were 11.5 versus 5.9 per 100 person-years before RYGB [RR = 1.95 (95% confidence interval (CI): 1.89-2.01)], increasing to 24.9 versus 7.1 per 100 person-years after RYGB [RR = 3.38 (95% CI; 3.30, 3.47)]. RRs of cardiovascular and chronic pulmonary disease admissions decreased considerably. RRs increased for alcohol abuse [0.59 (95% CI; 0.39-0.88) to 2.17 (95% CI; 1.72-2.72)], self-harm (suicide attempts, medication overuse) [1.72 (95% CI; 1.32-2.25) to 3.61 (95% CI; 2.88-4.52)], anemia [0.84 (95% CI; 0.39-1.78) to 17.92 (95% CI; 14.94-21.48)], and osteoporosis [1.19 (95% CI; 0.93-1.53) to 1.65 (95% CI; 1.35-2.02)]. Short-term surgical complications occurred in 3% and long-term complications in one-fourth of RYGB patients. Compared with the general population, the RR for any inpatient admission increased after RYGB.