Experiments were performed on 15 Sprague-Dawley rats to detect the effect of artificial ventilation of different frequencies on the high frequency component of heart rate variability (HRV) by autoregressive modeling with Burg algorithm. With continuous or intermittent electrical stimulation, different patterns of regulating activity of nucleus ambiguus in medulla on HRV were observed. Fast Fourier transform was used to analyze the coherence between neuronal discharge with respiratory rhythm in rostral ventrolateral medulla (rVLM) and HRV. The results showed that (1) the central frequency of high frequency (HF) component of HRV were moved closely with frequencies of artificial ventilation, (r = 0.83, P < 0.0001); (2) there was a favorable coherence between neuronal discharge with respiratory rhythm in rVLM and HRV in HF on spectrum, (k2 = 0.854 +/- 0.1); (3) the area of HF component in HRV was increased significantly during intermittent electrical stimulation of nucleus ambiguus in medulla. The central frequency of HF component in HRV was influenced mainly by frequencies of respiration. These results indicate a significant correlation between the HF in HRV and neuronal discharge with respiratory rhythm in rVLM, suggesting that rVLM participates in the regulation of HRV. The HF component of HRV may reflect mainly the fluctuating activity of vagal center. Coherence analysis of two signals provides a new method to confirm the type and interaction of neurons in the central cardiovascular system.