The long-term safety of geological disposal systems for high-level radioactive wastes will depend in part on the retention behavior of any elements that are released from the waste in the surrounding host rocks. The retention of rare earth elements (REE),thorium (Th),and uranium (U) in deep sedimentary formations of the Horonobe area, Hokkaido, Japan (the Koetoi and Wakkanai Formations) was investigated in the present investigation as a case study. The REE and Th in the Koetoi and Wakkanai Formations appear to be retained in clay, aluminosilicate and phosphate minerals. The distribution of these elements is relatively homogeneous in both formations. Uranium was sorbed by organic matter or was precipitated in secondary minerals under reducing conditions during initial sedimentation and/or later diagenesis. Changes in hydrogeological or rock facies conditions appear to have no impact on the retention behavior of the REE, Th, and U. These observations suggest that such retention behavior can be effective over very long periods of time. The results of the present study are thus consistent with those of previous investigations, which indicate that sedimentary formations in the Horonobe area have effectively attenuated radionuclide transport due to a reducing environment in a chemically closed system.