To evaluate representative elemental composition of agricultural soils in Japan and to investigate the relationship between elemental composition of agricultural soils and their soil type, land use and region in Japan, 180 soil samples were collected from the surface layer of paddy or upland fields in Japan and their total contents of 20 elements were determined. Total concentrations of aluminum (Al), iron (Fe), calcium (Ca), magnesium (Mg), titanium (Ti), phosphorus (P), manganese (Mn), barium (Ba), vanadium (V), strontium (Sr), zinc (Zn), copper (Cu) and nickel (Ni) were determined by ICP-AES and those of potassium (K) and sodium (Na) by atomic absorption spectrophotometry after wet digestion of the finely ground samples with nitric acid (HNO3), hydrofluoric acid (HF) and perchloric acid (HClO4). Total concentration of selenium (Se) was determined by HPLC after treatment of the wet digested solution (HNO3 and HClO4) of the samples with 2,3-diaminonaphthalene and extraction with cyclohexane. Total concentrations of carbon (C) and nitrogen (N) were determined by the dry combustion method, and those of silicon (Si) and oxygen (O) were determined by calculation. The medians of the total concentrations of the 10 major elements were 504 g O kg−1, 291 g Si kg−1, 76.6 g Al kg−1, 36.8 g Fe kg−1, 24.8 g C kg−1, 15.0 g K kg−1, 14.3 g Na kg−1, 11.9 g Ca kg−1, 8.78 g Mg kg−1 and 3.82 g Ti kg−1, which accounted for 98.7% of the total. The medians of the others were 2.15 g N kg−1, 1.43 g P kg−1, 705 mg Mn kg−1, 394 mg Ba kg−1, 140 mg V kg−1, 125 mg Sr kg−1, 90.5 mg Zn kg−1, 24.5 mg Cu kg−1, 14.3 mg Ni kg−1 and 0.42 mg Se kg−1. In terms of soil type, volcanic soils had relatively high Al, Fe, C, N and P contents and alluvial soils had relatively high Si, K and Ba contents, whereas red yellow soils had extremely low Ca, Mg and Na contents. In terms of land use, upland soils had significantly higher Al, Fe, C, Ca, Mg, Ti, N, P, Mn, V and Se contents and lower Si, K and Ba contents than paddy soils. Cluster analysis of elemental composition of agricultural soils grouped regions in Japan into three groups: (1) Okinawa region, (2) Hokkaido, Tohoku, Kanto, Chugoku and Kyushu regions, and 3) Hokuriku-Chubu, Kinki and Shikoku regions, reflecting their soil types. In conclusion, these data can be used as basic information on which development of sustainable agriculture and promotion of environmental conservation is to be established.