Neonatal maternal separation has been found to affect adult brain function. However, the molecular basis has not been clarified. The purpose of this study was to elucidate the changes in mineral levels related to the antioxidative system in the adult mouse hippocampus after neonatal maternal separation. Male mouse pups in the maternal separation group were separated from their dams for 3 hours daily during the first 2 postnatal weeks. The hippocampal selenium, calcium, zinc, copper, and manganese contents were analyzed with an inductively coupled plasma mass spectrometer at 13 postnatal weeks, and plasma protein carbonyl and 8-OHdG concentrations were examined by enzyme-linked immunosorbent assay. It was found that the hippocampal selenium content was about three times lower in the maternal separation group than that in the control group, representing a significant difference. The hippocampal calcium content was more than 2 times higher in the maternal separation group than that in the control group. The plasma protein carbonyl concentration was about seven-fold higher in the maternal separation group than that in the control group. However, no significant differences were found in the hippocampal calcium, zinc, copper, and manganese contents, or in plasma protein carbonyl and 8-OHdG concentrations between the maternal separation and control groups. Therefore, neonatal maternal separation affects the hippocampal selenium content of adult male mice, but does not affect other mineral contents, such as zinc, copper, manganese, and calcium in the hippocampus.