An elucidation of the background levels of heavy metals, including certain toxic elements, is very essential to accomplish an important environmental assessment. A regional geochemical mapping in Hokkaido, Japan was undertaken by the Geological Survey of Japan, AIST as part of a nationwide geochemical mapping for this purpose. There were 692 stream sediments collected from the active channel (1 sample) / (100 km 2) in Hokkaido and the fine fraction sieved through a 180 μm screen was analyzed using the AAS, ICP-AES, and ICP-MS techniques. The regional geochemical maps for 51 elements were created as a 2000 m mesh map using the geographic information system software. Spatial distribution patterns of elemental concentrations in stream sediments, particularly Neogene–Quaternary volcanic and pyroclastic rocks, are primarily determined by surface geology. The correspondence of elemental concentrations in stream sediments to parent lithology is clearly indicated by ANOVA and a multiple comparison. Sediment samples supplied from mafic volcanic and felsic–mafic pyroclastic rocks are significantly rich in MgO, Al 2O 3, P 2O 5, CaO, Sc, TiO 2, V, MnO, Total (T)-Fe 2O 3, Co, Zn, Sr, and heavy rare earth elements (REEs) (Y and Eu–Lu), but significantly lacking in alkali elements, Be, Nb, light REEs (La–Nd), Ta, Tl, Th, and U. Accretionary complexes with sedimentary rocks derived from sediments are in stark contrast to volcanic and pyroclastic rocks. Accretionary complexes with mafic–ultramafic rock have significantly elevated Nb, Ta, and Th abundances in sediments besides MgO, Cr, Ni, Co, and Cu. This inexplicable result is caused by the mixed distributions of granite and ultramafic–mafic rocks. The watersheds with mineral deposits relate to the high concentrations of certain elements such as Zn, As, and Hg. The geochemically anomalous pattern, which is a map of the regional anomalies, and a scatter diagram were applied to examine the contribution of mineral deposits to MnO, T-Fe 2O 3, Cr, Cu, Zn, As, Cd, Sb, Hg, Pb, and Bi concentrations. Consequently, they were grouped into four types: 1) Mineral deposits with no outliers resulting from mineralization (MnO, T-Fe 2O 3, and Cr), 2) sediments supplied from watersheds without metal deposits conceal high metal inputs from known mineral deposits (Cu), 3) deposits from a geochemically anomalous area that closely relates to the presence of mineral deposits (As, Sb, and Hg), and 4) deposits from the widely altered zone associated with the Kuroko as well as hydrothermal deposits corresponding to geochemically anomalous patterns (Zn, Cd, and Pb). This study provides an important regional geochemical database for a young island-arc setting and interpretational problems, such as complicated geology and active erosion, that are unique to Japan.