Paced breathing is a frequently performed technique for cardiovascular autonomic studies. The relative timing of inspiration and expiration during paced breathing, however, is not consistent. We, therefore, examined whether indexes of heart rate variability and spontaneous baroreflex sensitivity would be affected by the respiratory time ratio that is set. We studied 14 healthy young adults who controlled their breathing rates to either 0.1 or 0.25 Hz in the supine and sitting positions. Four different inspiratory-to-expiratory time ratios (I/E) (uncontrolled, 1:1, 1:2, and 1:3) were examined for each condition in a randomized order. The results showed spectral indexes of heart rate variability and spontaneous baroreflex sensitivity were not influenced by the I/E that was set during paced breathing under supine and sitting positions. Porta's and Guzik's indexes of heart rate asymmetry were also not different at various I/E during 0.1-Hz breathing, but had larger values at 1:1 during 0.25-Hz breathing, although significant change was found in the sitting position only. At the same time, Porta's and Guzik's indexes obtained during 0.1-Hz breathing were greater than during 0.25-Hz breathing in both positions. The authors suggest that setting the I/E during paced breathing is not necessary when measuring spectral indexes of heart rate variability and spontaneous baroreflex sensitivity under the conditions used in this study. The necessity of paced breathing for the measurement of heart rate asymmetry, however, requires further investigation.