We compared the effect of nesiritide and dobutamine on heart rate variability (HRV) in decompensated heart failure. In the nesiritide group, patients with severely depressed HRV displayed a significant increase in the indices of total variability (SDNN and SDANN5) and parasympathetic modulation (RMSSD). No changes occurred in patients with moderately depressed HRV at baseline. In the dobutamine group, patients with moderately depressed HRV at baseline had a reduction in SDNN, SDANN5, pNN50, and RMSSD. With severely depressed HRV, no further reduction in overall HRV or vagal modulation occurred. Conclusion: Nesiritide improves overall HRV and parasympathetic modulation in patients with severely depressed HRV and has no adverse effect on patients with relatively preserved HRV. In contrast, dobutamine reduces or has no effect on overall variability and parasympathetic modulation.