Purpose Deep breathing assesses autonomic function; however, many researchers/clinicians do not account for hyperventilation, brain blood flow or blood pressure. Methods Men and women (with/without oral contraceptives) participated. women participated during low and high hormone phases of the menstrual cycle. Blood pressure, end-tidal carbon dioxide, middle cerebral artery velocity and cerebrovascular resistance were assessed. Results Deep breathing decreased end-tidal carbon dioxide and middle cerebral artery velocity while increasing cerebrovascular resistance in all participants; blood pressure decreased in men. There were no influences of menstrual cycle or oral contraceptives. Conclusions Men have different autonomic responses to deep breathing compared to women.