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Little is known about the effects of the menstrual cycle on brain activity in primates. Here, we use 18F-fluorodeoxyglucose positron emission tomography to monitor changes in resting brain glucose metabolism across the menstrual cycle in female rhesus monkeys. Results showed greater activity in right lateral orbitofrontal cortex, a region involved in processing negatively valenced emotional stimuli, in the follicular compared with luteal phase. Estradiol levels were negatively correlated with activity in cortical and brainstem regions involved in emotional processing, and positively correlated with activity in areas involved in cognitive control and emotion regulation. In summary, the data suggest that in primates, fluctuations of ovarian hormones across the menstrual cycle influence activity in brain areas involved in emotion and its regulation.