Heart rate variability (HRV) is a validated measure of sympato-vagal balance in the autonomic nervous system. HRV appears decreased in patients with bipolar disorder (BD) compared with healthy individuals, but the extent of state-related alterations has been sparingly investigated. The present study examined differences in HRV between affective states in BD. A heart rate and movement sensor weighing 8 g collected average acceleration, heart rate and the two slowest and fastest heart beats (of the most recent 16 beats) every 30 s over a period of at least three consecutive weekdays and nights in a prospective longitudinal design from a total of 31 different affective states in 16 outpatients with BD. A proxy measure of HRV was calculated as the difference between the second-shortest and the second-longest inter-beat-interval collected during each of the epochs. Analyses were based on over 100.000 HRV data-points. In unadjusted analyses and in analyses adjusted for age, gender and heart rate, during a manic state HRV was increased by 18% compared with a depressed state (eB = 1.18, 95% CI: 1.16-1.20, p < 0.001) and increased by 17% compared with a euthymic state (eB = 1.17, 95% CI: 1.15-1.19, p < 0.001), whereas there was no difference between a depressive state and a euthymic state (eB = 0.98, 95% CI: 0.96-1.00, p = 0.12). Further inclusion of BMI as a covariate did not alter any of the associations. HRV appears to be altered in a state-dependent manner in bipolar disorder and could represent a candidate state marker. Further studies with larger sample sizes are warranted.