Respiration influences heart rate variability, leading to the suggestion that respiration should be controlled to assess autonomic function by using heart rate variability. Clearly, control of respiration is advantageous or even essential in several experimental circumstances. However, control of respiration, by itself, produces a small, but significant, increase in mean heart rate and a decrease in respiratory synchronous variation in heart rate. We tested whether, in some experimental situations, it may be possible to arrive at similar interpretation about autonomic function with and without using control of respiratory rate. Heart rate spectral powers from nine subjects were compared between spontaneous and metronomic breathing during two sympatho-excitatory stresses, lower body negative pressure (LBNP) and head up tilt (HUT). The normalized spectral powers in supine and HUT during spontaneous breathing were: 0.43 and 0.75 in very low (VLF) and 0.28 and 0.09 in high frequency (HF) regions. The powers during metronomic breathing were: 0.36 and 0.82 (VLF) and 0.36 and 0.09 (HF). The powers in supine and LBNP during spontaneous breathing were: 0.43 and 0.81 (VLF) and 0.28 and 0.06 (HF). The powers during metronomic breathing were: 0.36 and 0.80 (VLF) and 0.36 and 0.07 (HF). All p values were <0.05. Therefore, changes in heart rate spectral powers during HUT and LBNP were similar during metronomic breathing and spontaneous breathing. These results suggest that in experimental designs such as in our study, using metronomic breathing may not provide any additional insight into autonomic function than that can be obtained during spontaneous breathing.