We studied heart rate (HR), heart rate variability (HRV) and respiratory sinus arrhythmia (RSA) in 4 male subjects before, during, and after 16-days of space flight. The electrocardiogram (ECG) and respiration were recorded during two periods of 4 minutes controlled breathing at 7.5 and 15 breath/min in standing and supine postures on ground and in microgravity (µG). Low (LF) and high (HF) frequency components of the short-term HRV (3min) were computed through Fourier spectral analysis of the RR intervals. Early in µG, HR was decreased compared to both standing and supine, and had returned to supine value by the end of the flight. In µG, overall variability, LF/HF ratio, and RSA amplitude and phase were similar to preflight supine values. Immediately postflight, HR increased by ~15% and remained elevated 15 days after landing. LF/HF was increased, suggesting an increased sympathetic control of HR standing. The overall variability and RSA amplitude in supine decreased postflight, suggesting that vagal tone decreased, which coupled with the decrease in RSA phase-shift suggests that this was the result of an adaptation of autonomic control of HR to µG. In addition these alterations persisted for at least 15 days after return to 1G.