The aim was to compare the distribution of ANCs in purple and blue corn coproducts from three conventional corn fractionation processes and linking ANC partitioning in different coproducts to corn kernel phenotype. Total monomeric anthocyanin (TA) from purple corn extract was 4933.1±43.4mg cyanidin-3-glucoside equivalent per kg dry corn, 10 times more than blue corn. In dry milled purple corn, maximum ANCs were present in the pericarp (45.9% of total ANCs) and in wet-milling they were concentrated in steeping water (79.1% of total ANCs). For blue corn, the highest TA was in small grits and gluten slurry in dry-milling and wet-milling coproducts, respectively. HPLC showed the highest concentration of each ANC in steeping water for purple corn coproducts. Micrographs of kernel showed pigments concentrated in pericarp layer of purple but only in aleurone of blue corn. ANCs can concentrate in certain coproducts depending upon physical distribution of pigments in kernel.