Background and objectives Weight loss is the mainstay of management for women with polycystic ovarian syndrome (PCOS). However, lifestyle and dietary modifications, and gastric banding have generally poor long-term efficacy. We aimed to investigate whether gastric bypass is equally efficacious in women with or without PCOS. Methods We performed a matched case–control study of primary Roux-en-Y gastric bypass surgery in women with PCOS (cases, n = 30) compared to women without PCOS (controls, n = 60) matched for baseline age, body mass index (BMI) and presence or absence of type 2 diabetes (T2D). Data shown represent mean values. Results At 24 months after surgery the 90 participants (age 36.1 years) experienced significant reductions in BMI (53.4 vs. 34.9 kg/m2, p Conclusion In women with PCOS with morbid obesity, gastric bypass resulted in significant weight loss and metabolic outcomes similar to women without PCOS.