Purpose To investigate the association between follicular fluid homocysteine levels and embryo quality and pregnancy rates in patients undergoing assisted reproduction. Methods Fifty infertile women who were admitted to our clinic were enrolled in the study. Ovulation induction was performed by using GnRH agonist and gonadotropins. For each patient, homocysteine level in the follicular fluid was measured by using nephelometric method after the oocyte pick-up. The association between the homocysteine concentration in the follicular fluid and the oocyte-embryo quality, pregnancy rates and hormone levels were investigated. Results Mean ± SD Hcy was 9.6 ± 2.02 μmol/L and 14.9 ± 2.93 μmol/L in pregnant and non-pregnant women, respectively (p<0.0001). There were no statistically significant differences between pregnant and non-pregnant women in mean age, duration of infertility, body mass index, the oocyte-embryo quality parameters, and hormone levels. Homocystein did not have any correlation with M2, late M2, and total number of oocytes, number of fertilized oocytes and transferred embryos,andembryoqualitygrade.Areaundercurve (AUC) of hcy for prediction of pregnancy failure was 0.922 (p = 0.0001, 95% Confidence interval 0.85-0.99). A threshold of 11.9 μmol/L of hcy had a sensitivity of 82%, specificity of 100%, positive predictive value of 100% and negative predictive value of 91.6%for prediction of pregnancy failure. The subgroup analysis in male factor infertility group (n = 28), showed that mean homocystein was 9.9 ± 2.44 μmol/L and 14.1 ± 2.72 μmol/L in pregnant and non-pregnant women, respectively (p = 0.002). Conclusion Low follicular fluid homocysteine level is associated with a better chance of clinical pregnancy. © 2012 Springer Science+Business Media, LLC.