© The Royal Australian and New Zealand College of Psychiatrists 2016.Objective: There is evidence that mood disorders are associated with impaired parasympathetic nervous system function and consequently increased morbidity and mortality. Our study addresses whether this impairment persists into remission in unipolar and bipolar disorders. Methods: Heart Rate Variability was measured in groups of subjects during remission, with Bipolar Affective Disorder I (n = 29), recurrent Major Depressive Disorder (n = 41) and a healthy control group (n = 38), during the bedtime period. Results: Heart Rate Variability was found to be lower in the bipolar and depression groups, compared with control subjects, using the Root Mean Square of Successive Distances variable, and lower in the depression group using the Standard Deviation of Normal to Normal variable and the Standard Deviation, Poincare Plot variable. Conclusion: Autonomic function during bedtime was impaired in subjects with Bipolar I and recurrent Major Depressive Disorder, despite clinical remission. This has significant implications for the morbidity and mortality of patients with major mood disorders.