BACKGROUND: This cross-sectional study was undertaken to evaluate the factors that relate to menstrual status (oligo-amenorrhoea versus eumenorrhoea) in polycystic ovary syndrome (PCOS). METHODS: A total of 234 women with clinical and biochemical features suggestive of PCOS underwent metabolic and hormonal evaluation. A forward stepwise logistic regression model was created based on the results to determine variables related to ovulatory status. RESULTS: Only follicular phase progesterone and estradiol (E2) were retained in the final model. This model correctly classified 80% of PCOS women by ovulatory status. Univariate analysis revealed no difference in progesterone between ovulatory groups but E2 was higher in anovulatory groups. This suggested interaction between progesterone and E2 and the single interaction variable (progesterone/E2) also classified 80% of women by ovulatory status correctly. CONCLUSION: The results suggest that a low ratio of progesterone to E2 is associated with menstrual irregularity and ovulatory status in PCOS.