There is a complex interplay between sleep, metabolism and the function of the endocrine system. A number of endocrine systems are modulated by either the homeostatic drive to sleep, or by the function of the circadian system. As a result, changes in sleep duration and quality have reciprocal effects on hormone secretion and metabolism. In return, sleep disturbance can result from secondary consequences of abnormal endocrine and metabolic function. Inborn errors of metabolism have been demonstrated to have varying effects. The manifestations of lysosomal storage disorders are primarily dependent on the location of substance deposition; resultant effects include disruption of central respiratory control and changes in airway configuration. Neurologic consequences of these disorders include cases of epileptiform discharges in sleep and case reports of non-narcolepsy associated cataplexy.