The dynamic interactions among physiological rhythms imbedded in the heart rate signal can give valuable insights into autonomic modulation in conditions of reduced outward attention. Therefore, in this study we analyzed the heart rate variability (HRV) in different levels of practice in Zen meditation (Zazen). Nineteen subjects with variable experience took part in this study. In four special cases we collected both HRV and respiration data. The time series were analyzed in frequency domain and also using the Continuous Wavelet Transform, which detects changes in the time domain and in the frequency domain simultaneously. The shifts in the respiratory modulation of heart rate, or respiratory sinus arrhythmia (RSA), reflect the different levels of practice among practitioners with variable experience in Zazen; in turn the modulation of the RSA may reflect changes in the breathing pattern as in the parasympathetic outflow related to the quality and focus of attention in each stage.