Methods are provided for treating a subject for a condition. In accordance with the subject methods, at least a portion of a subject's autonomic nervous system is modulated during at least one predetermined phase of the subject's menstrual cycle to alter the parasympathetic activity/sympathetic activity ratio in a manner that is effective to treat the subject for the condition. The subject methods find use in the treatment of a variety of different conditions, including various disease conditions, that increase in severity and/or occurrence during one or more phases of the menstrual cycle. Also provided are systems and kits for use in practicing the subject methods.