Background: Vitamin D deficiency is prevalent among women, including patients with polycystic ovary syndrome (PCOS). Some studies have suggested that vitamin D may have a role in cardiovascular disease (CVD). There is very limited data on the vitamin D effect on CVD risk factors in women with PCOS and vitamin D deficiency. Aim: To investigate the effect of cholecalciferol on CVD risk factors in PCOS women with vitamin D deficiency. Methods: The study was a randomized, placebo-controlled, double blinded trial. Fifty PCOS women with vitamin D deficiency (vitamin D, no.=24; placebo, no.=26) aged 20–40 yr, were randomly assigned to receive 3 oral capsules of 50, 000 IU vitamin D3 or a placebo (one capsule every 20 days) for two months. Serum vitamin D, PTH, lipid profile, apolipoprotein AI (APO-AI), and high sensitive C- reactive protein (hs-CRP) were measured at baseline and after treatment. Results: Vitamin D3 therapy in PCOS patients, increased serum vitamin D (7.00±2.80 to 22.9±6.14 ng/ml), decreased serum total cholesterol (196.6±32.8 to 179.1±34.1 mg/dl), triglyceride (156.8±73.0 to 130.5±56.5 mg/dl), and VLDL (31.4±14.6 to 26.1 ±11.3 mg/dl) levels significantly (p<0.05), but it did not affect serum HDL-cholesterol, LDL-cholesterol, APO-AI, and hs-CRP concentrations. There was no change in variables in the placebo group. Conclusions: Our study showed that vitamin D3 therapy had beneficial effects on some CVD risk factors in PCOS patients with vitamin D deficiency. The trial was registered at IRCT.ir (IRCT138904113140N2).