Abstract Selenium is an essential element for humans, animals and some species of microorganisms. The biological function of selenium shows dual characteristics. The selenium content range between toxic and deficient concentration is very narrow. The present paper discusses the geographical distribution of two forms (total and water-soluble) of selenium in topsoil (plough layer for cultivated soils, eluvial horizon for natural soils) and evaluates its relationship with some human health problems in China. Topsoil samples, 354 in total, including 156 natural and 198 cultivated soils of 21 main soil types were collected. The total Se concentration in soil samples was determined with DAN (diaminonaphthalene)-fluorescence spectrophotometer method. Soil water-soluble Se concentration was determined with the same method after extraction with water (water/soil=5:1). The results showed that the geometric and arithmetic means of total Se concentration in soil, for all samples, were 0.173 mg/kg and 0.239 mg/kg, respectively, with the lowest value being 0.022 mg/kg and the highest being 3.806 mg/kg. For the cultivated soil, the geometric mean of total Se was 0.188 mg/kg, its arithmetic mean was 0.269 mg/kg and higher than those in the natural soil, 0.154 mg/kg and 0.206 mg/kg, respectively. The geometric and arithmetic means of water-soluble Se in soil for all the samples were 4.0 and 6.4 μg/kg, the lowest 0.6 μg/kg and the highest value being 109.4 μg/kg. For the cultivated soils, the average concentration of water-soluble Se was 4.3 μg/kg, similar to that of natural soil, they are and 4.4 μg/kg by geometric mean. Two sequences of the soil types, arranged separately in the concentration of total Se and water-soluble Se, are different and this demonstrates that the proportions of the two forms of selenium existing in various soils are different. The percentages of water-soluble Se to total Se in different types of soils varied from 1.07 to 6.69%. However, generally the laterite and other subtropic soil still have relatively high absolute water-soluble Se contents because of their higher total Se contents. A very significant correlation between total Se and water-soluble Se has been found in cultivated soil with a correlation coefficient of 0.58 ( P<0.001). The relationships between soil Se and human endemic diseases Keshan disease, Kashin–Back diseases and selenosis have been discussed. The reference criteria for evaluating Se deficiency and Se excess in soil were suggested.