Objectives Polycystic ovary syndrome (PCOS) is a common reproductive endocrine disorder associated with infertility, cardiovascular disease and type 2 diabetes. Despite anecdotal evidence that lesbians may have higher PCOS rates than heterosexuals, little empirically based evidence supports this theory. To address this gap, we examined PCOS prevalence and associated factors among a community sample of lesbian and heterosexual women. Methods Lesbian ( n = 114) and heterosexual ( n = 97) women aged 35 to 45 who participated in The Epidemiologic STudy of HEalth Risk (ESTHER) Project (Pittsburgh, PA) were recruited into our PCOS exploratory study between April and October 2008. A reproductive endocrinologist, “blinded” to participant sexual orientation, identified women with PCOS using a modified version of the 2003 Rotterdam Diagnostic Criteria for PCOS. Sexual orientation was defined by self-reported sexual identity, behavior, and attraction. Fisher’s exact, chi-square, and Wilcoxon rank-sum tests were used for analysis. Results Approximately 6.2% ( n = 13) of the total sample ( n = 211) had PCOS. PCOS rates did not significantly differ between lesbian and heterosexual women ([7.9%, n = 9] vs. [4.1%, n = 4]; p = .256). No significant differences in PCOS-related factors were found between lesbian and heterosexual women: polycystic ovaries ([10.5%, n = 12] vs. [6.2%, n = 6]; p = 0.261), hirsutism ([24.6%, n = 28] vs. [15.5%, n = 15]; p = 0.102), oligomenorrhea ([3.6%, n = 4] vs. [5.4%, n = 5]; p = 0.735), adult acne ([21.1%, n = 24] vs. [24.7%, n = 24], p = 0.524), and median testosterone ([1.69 ng/mL, n = 114] vs. [1.52 ng/mL, n = 97]; p = 0.069) and androstenedione ([1.63 ng/mL, n = 114] vs. [1.51 ng/mL, n = 97]; p = 0.079) concentrations, respectively. Conclusion PCOS and related factors did not differ by sexual orientation. Despite this, our observed rates warrant the need for additional studies to examine the relationship between PCOS diagnoses, PCOS-related factors, and sexual orientation.