Normally at rest the amplitude of respiratory sinus arrhythmia (RSA) appears to correlate with cardiac vagal tone. However, recent studies showed that under stress, RSA dissociates from vagal tone, indicating the possible existence of separate mechanisms regulating phasic and tonic vagal activity. This dissociation has been linked to the hypothesis that RSA improves pulmonary gas exchange through preferential distribution of heartbeats in inspiration. We examined the effects of hypercapnia and mild hypoxemia on RSA-vagal dissociation in relation to heartbeat distribution throughout the respiratory cycle in 12 volunteers. We found that hypercapnia, but not hypoxemia, was associated with significant increases in heart rate, tidal volume, and RSA amplitude. The RSA amplitude increase remained statistically significant after adjusting for respiratory rate, tidal volume, and heart rate. Moreover, the RSA amplitude increase was associated with a paradoxical rise in heart rate and decrease in low frequency to high frequency mean amplitude ratio derived from spectral analysis, which is consistent with RSA-vagal dissociation. While hypercapnia was associated with a significant increase in the percentage of heartbeats falling in inspiration, this was largely secondary to increases in the inspiratory period to respiratory period ratio, rather than RSA amplitude. Additional model analyses of RSA were consistent with the experimental data. No changes in heartbeat distribution occurred during hypoxemia. These results support the concept of RSA-vagal dissociation during hypercapnia, however the putative role of RSA in optimizing pulmonary-perfusion matching requires further experimental validation.