Polycystic ovary syndrome (PCOS) is an endocrine abnormality with multiple diagnostic criteria due to its heterogenic manifestations. One of the diagnostic criteria includes analysis of ultrasound images of ovaries for the detection of number, size, and distribution of follicles within the ovary. This involves manual tracing and counting of follicles on the ultrasound images to determine the presence of a polycystic ovary (PCO). We describe a novel method that automates PCO detection. Our algorithm involves segmentation of follicles from ultrasound images, quantifying the attributes of the automatically segmented follicles using stereology, storing follicle attributes as feature vectors, and finally classification of the feature vector into two categories. The classification categories are: PCO present and PCO absent. An automatic PCO diagnostic tool would save considerable time spent on manual tracing of follicles and measuring the length and width of every follicle. Our procedure was able to achieve classification accuracy of 92.86% using a linear discriminant classifier. Our classifier will improve the rapidity and accuracy of PCOS diagnosis, reducing the risk of the severe complications that can arise from delayed diagnosis.