Magnesium (Mg) deficiency is well known to affect metabolism of some trace minerals. We investigated the effect of Mg deficiency on hepatic concentration of various minerals in rats. Twelve 5-week-old male rats were divided into the groups given a control diet and an Mg-deficient diet. After 4 weeks, liver sample was collected from each rat. The concentrations of 36 minerals were simultaneously determined by a semiquantitative method of inductively coupled plasma-mass spectrometry (ICP-MS). The semiquantitative analysis showed that Mg deficiency significantly increased iron (Fe), copper (Cu), zinc (Zn), gallium (Ga), yttrium (Y), zirconium (Zr), molybdenum (Mo), rhodium (Rh), silver (Ag), and barium (Ba) concentrations, and significantly decreased scandium (Sc) and niobium (Nb) concentrations in rat liver. Then, hepatic Fe, Cu, Zn, Sc, Zr, and Mo concentrations were quantitatively measured, which indicated the similar effects as observed by the semiquantitative analysis. Additionally, the semiquantitative measurements of these minerals were highly correlated to these measurements with the quantitative method, but the measurements were not completely consistent between these analyses. The present study is the first research indicating the changes of hepatic Ga, Y, Zr, Mo, Rh, Ag, Ba, Sc, and Nb concentrations in Mg-deficient rats. The present study also indicates that the semiquantitative analysis with ICP-MS is a valid method for screening analysis to investigate various mineral concentrations in animal tissues.