Polycystic ovary syndrome (PCOS) has recently been linked with genomic instability and DNA damage. The aim of this study was to test genomic damage in women PCOS, using two different methods for assessing damage in both chromosome and base level. The study was performed on 36 newly diagnosed women with PCOS and 29 healthy women as controls. The micronucleus (MN) analysis used as a biomarker of chromosomal/DNA damage was performed in peripheral lymphocytes by cytokinesis-block method. 8-hydroxydeoxyguanosine (8-OHdG) levels used as a reliable marker of oxidative DNA damage were measured in plasma using an ELISA kit. We found that MN frequencies obtained from lymphocytes of the women with PCOS were significantly higher than those of controls (4.1 +/- 1.0 vs. 2.1 +/- 0.6, P = 0.001), whereas, no differences in 8-OHdG level were found between the patients with PCOS and controls (0.5 +/- 0.3 vs. 0.5 +/- 0.2, P = 0.858). These findings indicate that women with PCOS seem to have increased genomic instability, but do not appear to have oxidative DNA damage despite the increased oxidative stress associated with PCOS.