Fluid inclusions in quartz from miarolitic cavities, quartz veins and hydrothermal-ore veins at the typical Miocene granite-plutons in Tsushima and Kofu, Japan, were analyzed by particle-induced X-ray emission (PIXE) to examine chemistries and behaviors of hydrothermal fluids from granite body in island arcs. Most inclusions in the miarolitic cavities from the Kofu granite were aqueous two-phase inclusions, and those from the Tsushima body were polyphase, aqueous two-phase, and vapor-rich inclusions. Transition-metals compositions (Mn, Fe, Cu, Zn, Ge, and Pb) of the initial hydrothermal fluids inferred from inclusions in the miarolitic cavities were several tens to hundreds of parts per million by weight (ppm) for the Kofu granite and several hundreds ppm to several wt.% for the Tsushima granite. The high concentrations of the Tsushima were probably caused by extreme boiling of hydrothermal fluids because of the shallow emplacement level. Transition-metals contents of polyphase inclusions from the ore veins were comparable to those from porphyry cooper deposit in Bingham, tin ore in Mole granite, and quartz -tourmaline-topaz vein in Cornwall granite.