Electrovestibulography (EVestG) recordings have been previously applied toward classifying and/or measuring the severity of several neurological disorders including depression with and without anxiety. This study’s objectives were to: (1) extract EVestG features representing physiological differences of healthy women during their menses, and follicular and luteal phases of their menstrual cycle, and (2) compare these features to those observed in previous studies for depression with and without anxiety. Three EVestG recordings were made on 15 young healthy menstruating females during menses, and follicular and luteal phases. Three features were extracted, using the shape and timing of the detected spontaneously evoked vestibulo-acoustic field potentials. Using these features, a 3-way separation of the 3 phases was achieved, with a leave-one-out cross-validation, resulting in accuracy of > 72%. Using an EVestG shape feature, separation of the follicular and luteal phases was achieved with a leave-one-out cross-validation accuracy of > 93%. The mechanism of separation was not like that in previous depression analyses, and is postulated to be more akin to a form of anxiety and/or progesterone sensitivity.