Objective: To evaluate the role of apolipoprotein C-I (apoC-I) levels and assess relationships between apoC-I and clinical features in women with polycystic ovary syndrome (PCOS). Design: Prospective study. Setting: Reproductive Center of Peking University Third Hospital. Patient(s): Thirty patients with PCOS with insulin resistance, 30 patients with PCOS without insulin resistance, and 30 control individuals. Intervention(s): Fasting serum samples. Main Outcome Measure(s): Measures of serum apoC-I, androgens, total cholesterol, triglycerides, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, apoA1, apoB, heat-shock C-reactive protein, glucose, and homeostasis model assessment of insulin resistance (HOMA-IR). Result(s): We found differentially expressed proteins by use of the surface-enhanced laser adsorption/ionization (SELDI) protein chip in the serum of women with PCOS and controls. Of these, apoC-I, was highly up-regulated. ApoC-I is associated with glycometabolism and lipid metabolism, but its role in PCOS has been unknown. The serum levels of apoC-I in the patients with PCOS were statistically significantly elevated compared with those of controls, especially in women with insulin resistance. The lean PCOS women had higher apoC-I levels than controls. In patients with PCOS and without any abnormal serum lipid index, apoC-I levels were still higher than in controls. Analysis showed that apoC-I correlated with body mass index, triglycerides, high-density lipoprotein cholesterol, apoA1, and HOMA-IR. Conclusion(s): ApoC-I may have an important role in glucose and lipid metabolism, and may be useful for early demonstration of metabolic abnormality in women with PCOS. © 2010 American Society for Reproductive Medicine.