Degassing of volatile elements are occurring trough volcano, hot spring and natural gas in the Japanese Islands. Among the volatiles, helium-3 is the most important nuclide to show the mantle signature. The ratio of helium-3 to helium-4 of crustal and/or radiogenic origin is a useful parameter to study tectonic setting of the region. Geographical distribution of the helium isotopes has been investigated since middle 1980s. On the other hand, recent advance of earthquake research makes precise seismic tomography. We present here complies of helium isotope data in Japan and discuss their relation to the sesimic tomography.