We carried out a case-control study to investigate the association between the risk of developing cystic ovaries and the concentrations of Se in the blood of dairy cows. Cows were from dairy herds in the vicinity of Ithaca, NY. One hundred and thirty-two cystic ovary cases were identified; a similar number of herdmates who did not have cystic ovaries were selected as controls. Whole blood samples were collected from cystic cows and controls in which Se concentrations were determined. Milk samples also were collected and analyzed for concentrations of progesterone. Multivariate logistic regression analysis was used to identify the role of Se in the risk of developing cystic ovaries while controlling for other possible risk factors. Mean Se in blood concentration for cows with cystic ovaries (141 ng/ml) was similar to that of control cows without cystic ovaries (136 ng/ml). The concentration of progesterone in milk was significantly higher in controls than in cows with cystic ovaries. In the multivariate logistic regression analysis, cows with concentrations of Se in blood greater than 169 ng/ml had twice the risk of developing cystic ovaries compared with cows that had Se levels less than 108 ng/ml.