The association of androgen excess with abdominal adiposity, insulin resistance and metabolic derangements characterize many patients with PCOS. However, the mechanisms underlying these associations are not entirely understood, indicating the need for discovery of the origin of these metabolic alterations, and of new metabolic biomarkers for PCOS. This review summarizes the metabolites and metabolic pathways associated with PCOS according to recent metabolomic studies. PCOS associated metabolites were involved mostly in carbohydrate, fat, and protein metabolism. Obesity, hyperinsulinemia and the intrinsic heterogeneity of PCOS are responsible of the metabolic variation observed in these women. Furthermore, treatment of PCOS seems to modify the levels of some metabolites. Hopefully, advances in the knowledge of metabolism will allow the detection of systemic imbalances in PCOS and will permit the identification of biomarkers that serve to predict the progression of the disease and its future complications.