The estrogen hormones have been shown to be highly glycogenic as well as lipolytic in nature. It is unknown whether the metabolic actions of estrogens impact upon energy metabolism during exercise. The composition of prior diet, however, does affect exercise energy metabolism. This study examined the influence of menstrual cycle phase (mid-follicular [FP; low estrogen] vs. mid-luteal [LP; high estrogen]) and diet composition on the rate of substrate oxidation for carbohydrate (CHO) and lipid at rest and during various intensities of physical exercise. Nine subjects completed an experimental session under four different menstrual cycle-diet conditions: 1) FP following a 3-day high CHO diet [75% total caloric intake], 2) FP following a 3-day low CHO diet [35% total caloric intake], 3) LP following a 3-day high CHO diet, and 4) LP following a 3-day low CHO diet. In each of the experimental sessions substrate oxidation was determined at rest and during cycle ergometer exercise at intensities of 30, 50, and 70% VO2max, respectively. Statistically significant (p < 0.05) interaction effects on substrate oxidation due to the menstrual cycle phase and diet conditions were found at rest and during 30%-50% exercise. In general, CHO oxidation was lowest and lipid oxidation highest in the LP under a low CHO diet condition.