As a rule, geological disposal is considered a safe method for final disposal of high-level radioactive waste. However, some long-lived fission products like 99Tc and 129I contained in spent nuclear fuel are highly mobile as less sorbing anionic species in the subsurface environment and can mainly cause exposure dose to the ecosystem by emission of beta rays in the hundreds of keV range. Therefore, if these two nuclides can be separated and converted with high efficiency into radioactively unharmful nuclides, this would have a positive effect on disposal safety. One candidate method is to transmute these two nuclides in nuclear reactors into short-lived nuclides or into stable nuclides. For this purpose, it is necessary to evaluate which reactor type is more efficient in burning these two nuclides. In this study, the simulation results of nuclear transmutation of 99Tc and 129I in light water reactor (PWR), heavy water reactor (CANDU) and fast neutron reactor (SFR, MET-1000) are compared and discussed.