Previous studies have indicated involvement of the thalamus and the pons in the KleineLevin syndrome. In the present study, we investigated functional connectivity of the thalamus and the pons in asymptomatic Kleine-Levin syndrome patients and healthy controls. Twelve patients and 14 healthy controls were investigated by functional magnetic resonance imaging during rest. Resting state images were analysed using seed regions of interest in the thalamus and the pons. Results showed significantly lower functional connectivity between the pons and the frontal eye field in persons with Kleine-Levin syndrome compared to healthy controls. There were no connectivity differences involving the thalamus. Based on these findings, we propose a relation between the sleep disorder Kleine-Levin syndrome and cerebral control of eye movements, which in turn is related to visual attention and working memory. This hypothesis has to be tested in future studies of oculomotor control in the Kleine-Levin syndrome.