The status of chronic fatigue syndrome (CFS) is still under debate. Mainstream views still often consider it as an undetected primary sleep disorder or as the psychosomatic expression of a related anxiety or depression syndrome. Both primary sleep disorder and CFS are often related to unrefreshing sleep and affective daytime symptoms. The present study compares nonrapid eye movement sleep distribution between patients with a primary sleep disorder and “pure” CFS patients without sleep or mood disorders. Intensity measures of affective symptoms are also analyzed. Sleep variables of 32 pure CFS (mean age, 41.9 ± 8.7 years; 25 women), 30 Sleep Apnea Hypopnea Syndrome patients (mean age, 43.7 ± 6.7 years; 13 women), and 14 healthy controls (mean age, 40.2 ± 7.6 years; 9 women) were compared. Related affective symptoms were assessed using the self-reported Zung anxiety and depression scales. The study confirms previous reports on increased slow-wave sleep in CFS patients. Both patient groups showed similar sleep duration and efficiency. Sleep efficiency was lower in both patient groups compared with controls. CFS patients showed a higher microarousal index than controls. Anxiety, but not depression symptoms were more intense in the CFS group. The distribution of nonrapid eye movement sleep in CFS differs sizeably from what can be observed in a primary sleep disorder.