A modified selenium (Se) fractionation procedure was used to study Se distribution in three soils (two silt loams and one silty clay). This sequential procedure consisted of: i) 0.2 M potassium sulfate (K2SO4)‐soluble fraction, ii) 0.1 M potassium dihydrogen phosphate (KH2PO4)‐exchangeable fraction, iii) 0.5 M ammonium hydroxide (NH3H2O)‐soluble fraction, iv) 6 M hydrochloric acid (HCl)‐extractable fraction, and v) residual fraction digested with perchloric (HClO4) and sulfuric (H2SO4) acids. The fractionation procedure had high recovery rates (92.5 to 106%). The Se distribution in soil was controlled by soil properties, such as pH, oxide, clay, and calcium carbonate (CaCO3) contents. In the untreated soil samples, residual Se fraction was dominant. In the Se‐enriched soils, the silty clay had significantly more Se in the NH3H2O and residual fractions while in the two silt loams the largest were KH2PO4 and residual fractions. The Se availability in the two silt loams was higher than in the silty clay. The Se availability pattern in the untreated soils was: unavailable (HCl + residual fractions) >> potentially available (KH2PO4 + NH3H2O fractions) > available (K2SO4 fraction), while in the Se‐enriched soils it was potentially available > unavailable > available.