AIM To examine the effect of gastric bypass surgery on cardiometabolic health among women with polycystic ovarian syndrome (PCOS). METHODS Retrospective medical chart review identified women (n = 389) with PCOS who underwent Roux-en-Y gastric bypass surgery from 2001-2009 in one surgical practice. Separate repeated measures linear mixed models were fit using the MIXED procedure to assess mean change in cardiometabolic disease risk factors from before to 1-year after surgery and were evaluated by ethnicity [Hispanic, non-Hispanic black (NHB) and white (NHW)]. RESULTS The majority of the sample was Hispanic (66%, 25% NHB, 9% NHW). Mean body mass index significantly improved 1 year post-surgery for all ethnic groups (45.5 to 35.5 kg/m(2) for Hispanics, 46.8 to 37.7 kg/m(2) for NHB and 45.7 to 36.7 kg/m(2) for NHW, P < 0.001). Among Hispanic women mean total cholesterol (198.1 to 160.2 mg/dL), low-density lipoproteins (LDL) cholesterol (120.9 to 91.0 mg/dL), triglycerides (148.6 to 104.8 mg/dL), hemoglobin A1c (6.2% to 5.6%), alanine aminotransferase (28.1 to 23.0 U/L) and aspartate aminotransferase (23.5 to 21.6 U/L) decreased significantly (P < 0.001). Among NHB, mean total cholesterol (184.5 to 154.7 mg/dL), LDL cholesterol (111.7 to 88.9 mg/dL) and triglycerides (99.7 to 70.0 mg/dL) decreased significantly (P < 0.05). Among NHW, mean total cholesterol (200.9 to 172.8 mg/dL) and LDL cholesterol (124.2 to 96.6 mg/dL), decreased significantly (P < 0.05). Pairwise ethnic group comparisons of all cardiometabolic outcomes adjusted for age and type of surgery before and 1 year after surgery showed no statistical difference between the three groups for any outcome. CONCLUSION Cardiometabolic disease risk improvements vary by ethnicity and obesity may impact glucose tolerance and liver function changes more in Hispanic women with PCOS vs non-Hispanic women.