This study aims to show the change of Heart Rate Variability(HRV) and Pulse wave velocity(PWV) on menstruation in women at college. Heart Rate Variability(HRV) and Pulse wave velocity(PWV) of 122 women at college were measured at their menstruation and ordinary period. SDNN, RMSSD, SDSD, HRV Index(%), stress resistance and cardiac activity were significantly higher at their menstruation than ordinary period, but Total Power and pNN50(%) were opposite. The automatic nervous system balance and physical stress were decreased in groups without dysmenorrhea than with one. PWV(E-R) and PWV(E-L) were much higher at menstruation than ordinary period. PTT(F-R) and PTT(F-L) were decreased in groups without dysmenorrhea than with severe one. We demonstrated that menstruation can effect on Heart Rate Variability and Pulse wave velocity and dysmenorrhea can cause the imbalance of autonomic nervous system.