Heterogeneities in homogeneous nucleation during solidification of fcc Al, bcc Fe, and hcp Mg are studied. For this propose, high temperature second nearest-neighbor modified-embedded atom method potentials are utilized in molecular dynamics simulations. The amorphous atoms in solidification is generally identified as liquid or noncrystalline solid by common neighbor analysis. However, when bond-orientational order parameters are applied, several crystalline like structures are identified prior to formation of crystalline solids. The presence of these ordered structures in the intermediate state between the liquid and solid initiates the nucleation. After nucleation started, hcp and fcc twin boundaries are identified in Al and Mg matrices. In Fe, liquid transformed into icosahedral (ico) phase first, and later transformed to bcc. During solidification, the twin boundaries in Al and Mg and the ico atoms in Fe behave like a second phase, and initiate heterogeneities in homogeneous nucleation.