Polycystic ovary syndrome (PCOS) has been consistently associated with subsequent gestational diabetes mellitus (GDM). Women with PCOS showed a high prevalence of obesity, which raises the question regarding the role of obesity or PCOS in development of GDM. In this study we conducted a 2-phase study to compare the risk of GDM and its associated early pregnancy metabolic factors in women with and without PCOS, stratified by pre-pregnancy body mass index (BMI).A 2-phase design was used in this study. The initial phase of the study included 566 age- and pre-pregnancy BMI-matched singleton pregnant women (242 with and 324 without PCOS). Risk of GDM and associated early-pregnancy risk factors were explored between women with and without PCOS, after stratification by pre-pregnancy BMI. Stratified analysis was conducted in normal weight (pre-pregnancy BMI < 25 kg/m) and overweight/obese (pre-pregnancy BMI ≥ 25 kg/m) groups. Subsequently, the findings was confirmed in a separate cohort study with 18,106 participants (877 with and 17,229 without PCOS).Overall, prevalence of GDM is higher in women with PCOS. Results from the initial study showed that in normal-weight subjects, there is a significant increase in GDM prevalence in PCOS women than non-PCOS women (26.5% vs. 16.2%, p = 0.02). Additionally, normal-weight PCOS women showed higher triglycerides levels (1.51 ± 0.84 mmol/L vs. 1.30 ± 0.75 mmol/L, p = 0.02), lower SHBG levels (277.8 ± 110.2 nmol/L vs. 330.5 ± 180.4 nmol/L, p = 0.001) and a possible trend towards higher insulin resistance (LogHoMA-IR 0.70 ± 0.55 vs. 0.57 ± 0.57, p = 0.05) during early pregnancy. However, in overweight/obese group, no difference in risk of GDM was observed between PCOS and non-PCOS subjects (p = 0.7). Results from the independent cohort confirmed the risk for GDM associated with PCOS in normal weight women (p < 0.0001).Consistent findings from the 2-phase study showed an increased risk of GDM in normal-weight, but not overweight/obese PCOS women. Analysis of early-pregnancy risk factors of GDM suggested that the pathogenesis of GDM in normal weight and overweight/obese women with PCOS may be different.