The higher levels of estrogen present during the pre-ovulatory (follicular) phase of the menstrual cycle lower BBTs. The higher levels of progesterone released by the corpus luteum after ovulation raise BBTs. The rise in temperatures can most commonly be seen the day after ovulation, but this varies and BBTs can only be used to estimate ovulation within a three day range.

If pregnancy does not occur, the disintegration of the corpus luteum causes a drop in BBTs that roughly coincides with the onset of the next menstruation. If pregnancy does occur, the corpus luteum continues to function (and maintain high BBTs) for the first trimester of the pregnancy. After the first trimester, the woman's body temperature drops to her pre-ovulatory normal as the placenta takes over functions previously performed by the corpus luteum.

Very rarely, the corpus luteum may form a cyst. A corpus luteum cyst will cause BBTs to stay elevated and prevent menstruation from occuring until it resolves, which could take weeks or months.

While avoiding pregnancy Charting of basal body temperatures is used in some methods of fertility awareness, and may be used to determing the onset of post-ovulatory infertility. However, BBTs only show when ovulation has occured; they do not predict ovulation. Normal sperm life is up to five days, making prediction of ovulation several days in advance necessary for avoiding pregnancy. BBT methods often use a rule similar to that from the Calendar Method to determine the beginning of the pre-ovulatory fertile phase.