Objective: Increased levels of homocysteine and C-reactive protein (CRP) are considered as independent risk factors for atherosclerosis. As the level of these factors is affected by sex hormones, a population-based assessment of their changes following oral contraceptive therapy is needed to avoid the side effects that might arise of these variations. To this aim, the present study was to investigate the effect combined oral contraceptive (OCP) on CRP and homocysteine levels among young healthy women. Methods: We conducted an observational cross-sectional analysis of 90 healthy, non-obese women (mean age 25 years and body-mass index 22 kg/m2). Forty-five healthy women on OCP and 45 healthy controls were studied for CRP and homocysteine levels by enzyme-linked immunosorbent assay (ELISA). Unpaired t test and Chi-square test were used for comparison of variables between oral contraceptive users and non-oral contraceptive users. Results: The results showed that the homocysteine (13.268±3.475 vs. 7.288±2.621 μmol/L) and CRP (5863.0±1349.5 vs. 1138.3±691.12 ng/ml) levels were significantly higher in women receiving OCP in comparison with the control group (p=0.027 and p<0.001, respectively). Conclusion: The alteration in homocysteine and CRP levels could be attributed to the OCP suggesting that use of these pills should be reviewed in women with increased risk of atherosclerosis and other cardiovascular risk factors.