Matrix diffusion is one of the important phenomena for evaluating the safety of the geological disposal of high level waste because it has an effect of retarding mass transport in crystalline rocks. Previous studies indicated that the altered granitic rocks have high retardation functions due to the micropore formation associated with hydrothermal alteration; however, there has not been enough knowledge on the matrix diffusion in weakly unaltered rocks (macroscopically unaltered rocks). Since the macroscopically altered granitic rocks in Japan are likely to be affected by deuteric alteration due to hydrothermal fluid resulting from crystallization of granitic magma, it is important to understand the effect of deuteric alteration on the matrix diffusion. Therefore, detailed observations were carried out to clarify the effects of deuteric alteration focused on the macroscopically unaltered granite sampled from 300m and 500m below ground levels at the Mizunami Underground Research Laboratory, central Japan. The results provide that the micropores are selectively formed in plagioclases due to deuteric alteration and they have the potential of acting as matrix diffusion paths. This is indicating the possibility that deuteric alteration can retard the mass transport in crystalline rocks in Japan. That plays a significant role in enforcing the barrier function of crystalline rocks.