The current study compares FDG uptake in the ovaries and uterus before and after chemotherapy with regard to the menstrual cycle and patient’s age. The FDG PET/CT studies of 182 women of reproductive age (12–50 years) referred for the assessment of various malignancies were evaluated. Patterns and degree of FDG uptake in the ovaries or uterus were correlated with patient’s age, chemotherapy and with the phase of the menstrual cycle. Physiological FDG uptake in ovaries of women <35 years who did not receive chemotherapy occurred with two peaks: at the beginning of menstrual cycle and at mid-cycle around ovulation. After chemotherapy, women <35 years showed FDG ovarian uptake during various stages of the menstrual cycle. In women >35 years, there was no difference in FDG ovarian uptake before and after chemotherapy. There was a negative relationship between the time elapsed from end of chemotherapy to the incidence of uptake in the ovary (p < 0.001). Bilateral ovarian uptake was significantly more prevalent in women < 35 years after chemotherapy (p < 0.01), with a significant negative dependence to time from the end of chemotherapy (p < 0.05). There was no statistically significant difference in FDG uptake in the uterus before and after chemotherapy in both age groups, as well as in SUVmax measurements in the ovaries and uterus. Chemotherapy may affect physiological FDG uptake in reproductive organs of women of reproductive age.