Objective: Polycystic ovary syndrome (PCOS) is a heterogeneous disorder characterized by hyperandrogenism, oligomenorrhea, and polycystic ovary morphology. Insulin resistance is a pathophysiologic contributor in 50~80% of women with PCOS. However, little is known about the effect of ovarian morphology on insulin resistance. Therefore we evaluated the relationships between polycystic ovary morphology and insulin resistance in women with PCOS. Methods: We recruited 787 women with PCOS diagnosed by National Institute of Child Health and Human disease (NICHD) criteria and 501 control women. In the early follicular phase, all subjects underwent venous blood sampling for glucose, insulin, and hormonal parameter after an overnight fast. The 75 g oral glucose tolerance test was performed, and insulin resistance was estimated as quantitative insulin sensitivity check index (QUICKI). Polycystic ovary morphology was diagnosed by 7-MHz transvaginal ultrasonography. Results: Women with PCOS were more obese and showed significantly higher fasting and post load 2hr glucose, fasting and post load 2hr insulin, and lower QUICKI than controls (all Ps < 0.001). In women with PCOS, ovarian volume and follicle number were positively correlated with free testosterone, fasting insulin and systolic blood pressure, and negatively correlated with mens number/year and QUICKI. Multiple regression analysis revealed that QUICKI was significantly associated with ovarian follicle number after adjustment for age, BMI, free testosterone, and mens number/year. But this association was not shown in controls. Conclusion: We identified that higher ovarian follicle number is associated with insulin resistance in women with PCOS. Ovarian follicle number could be an important indicator to decide further evaluation for insulin resistance.