To test the hypothesis that hypoxia and hypercapnia have different effects on the genesis of respiratory sinus arrhythmia (RSA), the magnitude of RSA to these stimuli was compared in 3 unanesthetized dogs. Respiration was continuously monitored through a permanent tracheostomy, and the electrocardiogram and blood pressure were also monitored. The magnitude of RSA was assessed as an instantaneous amplitude of the R-R interval oscillation in the high-frequency band of 0.15-0.80 Hz by means of complex demodulation. In a total of 47 runs with hypoxia, heart rate, mean arterial pressure, respiratory rate and tidal volume increased, but RSA magnitude decreased even after adjusting for the effects of respiratory rate and tidal volume. In a total of 39 runs with hypercapnia, heart rate and mean arterial pressure did not change, despite the increased respiratory rate and tidal volume. In contrast to hypoxia, RSA magnitude increased even after adjusting for the effects of respiratory rate and tidal volume. The different effects of the two respiratory stimuli on RSA magnitude were noted at any level of ventilation and support the original hypothesis. (Jpn Circ J 2001; 65: 738 - 742)