Prefrontal regions are involved in processing emotional stimuli and are a topic of interest in clinical and neurological research. Although sex steroids are potent neuromodulators, the influence of menstrual cycle phase and hormonal contraceptive use is rarely taken into account in neuroimaging studies. Our purpose was to evaluate changes in gamma-aminobutyric acid (GABA) in women, as measured by magnetic resonance spectroscopy (MRS), with phases of the menstrual cycle and use of hormonal contraceptives, and to assess correlations with premenstrual symptoms.Three MRI sessions per cycle were obtained in the natural cycle group, and two sessions in the hormonal contraceptives group. In addition to an anatomical scan, single voxel MRS in the prefrontal area was performed. After quality control, 10 women with natural cycle and 21 women taking hormonal contraceptives were included for analysis. Peripheral blood samples were obtained to determine endogenous hormone concentrations. Subjects were asked to complete a daily rating of severity of problems questionnaire, to quantify premenstrual symptoms. In the natural cycle group, we found a significant increase in prefrontal GABA concentration at the time of ovulation. Conversely, in the hormonal contraceptives group, no differences were found between the pill phase and pill-free phase. GABA concentrations did not significantly correlate with endogenous hormone levels, nor with premenstrual symptoms. Our results indicate that spectroscopically measured GABA concentrations are higher during ovulation in women with a natural menstrual cycle. We suggest that neuroimaging studies should take into account this variability.