Objectives: To acquire fundamental knowledge on menstrual cycle and its intraindividual variation in healthy Japanese female students and their association with biological attributes, lifestyle and food habit. Methods: We asked female students of a nursing school to keep a diary of their menstruation over 5 consecutive months and to fill a questionnaire on their biological attributes, lifestyle and consumption frequency of some food items during the period from November 2012 to January 2014. Results: The mean±standard deviation (SD) of cycle lengths of 180 women (20.4±0.9yrs) was 34.2±10.5 days. Of these 180 women, 141 had a cycle length within the normal range (25–38 days) while 10 had a shorter cycle and 20 had a longer cycle. The intraindividual variations of the cycle, defined as “range” (difference between the longest and shortest cycles of an individual) and “SD” (SD of mean of multiple lengths within an individual), were 11.4±10.3 and 7.9±11.8 days, respectively. Of 177 women, 73 and 109 had normal range and SD (≤6 days), respectively. The mean age of women with long cycles was older than that of women with short cycle (Kruscal-Wallis test, p<0.05), and women with greater intraindividual variations were older than those with small variations (U-test, p<0.05). Subjects with menstrual pain had greater “SD” than did those without pain (Chi-square test, p<0.05). Neither lifestyle nor food habit was associated with the length and intraindividual variations of the menstrual cycle. Conclusions: The present results provided fundamental knowledge on the length and intraindividual variations of the menstrual cycle and the sources of these variations in female Japanese university students.