This study examined the properties of the Beck Depression Inventory-II (BDI-II) in a sample of 111 patients with chronic fatigue syndrome (CFS). Exploratory factor analysis identified two factors. The mean score for the Somatic-Affective factor was significantly higher than the Cognitive factor. Convergent and discriminant validity were assessed for BDI-II total score, the two factor scores, and the BDI for Primary Care (BDI-PC). The BDI-PC and Cognitive factor demonstrated superior validity. Results suggest patients endorse BDI-II somatic items that overlap with CFS symptoms at a high rate. Factor scores should be evaluated separately, or the BDI-PC should be utilized with this population.