Increased carotid arterial stiffness is associated with a risk factor of congestive heart failure. Thus factors that affect carotid arterial stiffness are of both physiological and clinical interest. The purpose of the present study was to examine the effects of regular aerobic exercise and menstrual cycle on carotid arterial stiffness in young female. The carotid β-stiffness index, an index of carotid arterial stiffness, was assessed in eight young female athletes (20.5 ± 0.4 years) and ten young female control subjects (21.3 ± 0.7 years). The carotid β-stiffness index was determined using ultrasound images of the common carotid artery with simultaneous recording of carotid arterial blood pressure by applanation tonometry. There was no difference in carotid β-stiffness index between the control and the athlete group both at the early follicular and the pre-ovulation phase of the menstrual cycle. On the other hand, the carotid β-stiffness index decreased from the early follicular phase to the pre-ovulation phase both in the control and the athlete group. These results suggest that carotid arterial stiffness in young females is not affected by regular aerobic exercise, but changes with the menstrual cycle, irrespective of exercise status.