Sleep complaints are frequently reported by patients with Marfan and Ehlers-Danlos syndrome (EDS). We examined the exact nature of sleep complaints in these patients. A representative sample of Marfan and EDS patients responded to a general sleep questionnaire, including the Epworth Sleepiness Scale (ESS) and the Medical Outcomes Study Short-Form 36 (SF-36) health-related quality of life (QOL) questionnaire. Fifteen Marfan patients and 9 EDS patients were evaluated and compared to 24 healthy controls, matched for age, sex and body mass index. Maintaining sleep was frequently disturbed in Marfan (40%, p < 0.04) as well as in EDS patients (56%, p < 0.01). Sleep apnea was exclusively reported by Marfan patients (27%, p = 0.03). Periodic limb movements were much more reported in EDS (67%, p = 0.02) than in Marfan (27%, p = 0.25) compared to controls (8%). Pain and back complaints were highly presented in both groups, but most pronounced in EDS patients (47% in Marfan versus 77% in EDS). No differences for the scores in the ESS were found. For all SF-36 questionnaire items, scores were much lower in patient groups, except for emotional problems. We found that sleep complaints were not rare in Marfan and EDS patients and correlated well with different QOL items. Our study calls for greater attention to the presence of apnea, pain and periodic limb movements in these patients.