Compromised sleep and increased sympathetic nervous system (SNS) activity are implicated in the pathogenesis of, and disparities in, cardiovascular disease. Parasympathetic dominance during sleep may be important for cardiovascular health. Sleep and autonomic balance influence immune activity which impacts atherogenesis. We evaluated relationships between autonomic balance during sleep and morning levels of the immune activating cytokines, C-reactive protein (CRP) and Interleukin 6 (IL-6). Ninety four (59 female) young adult African Americans without medical conditions and substance use disorders spent two consecutive nights in a clinical research unit for sleep recordings and blood drawing on awakening. Cardiac tracings from the 2 nd sleep recording were analyzed for heart rate variability (HRV). BMI was the only non-HRV measure correlated with cytokine levels. Indicators of SNS activity for the pre-sleep, and first non-REM and REM sleep periods were independently correlated with morning IL-6 levels. Altered autonomic balance during sleep may be a modifiable factor that influences immune activation.