Blue maize is an excellent source of bioactive components such as phenolic acids and anthocyanins but when it is processed for human consumption, these compounds decrease considerably. Therefore, blue maize could be directed to produce nutraceutical extracts. The aim of this study was to evaluate the relation between anthocyanins composition of acidified and non-acidified extracts from native and hybrid blue maize genotypes and their antiproliferative effect in mammary (MCF7), liver (HepG2), colon (Caco2 and HT29) and prostate (PC3) cancer cells. The most abundant phenolic acid was ferulic acid. Nine anthocyanins were quantified in the extracts, being Cy3-Glu the most abundant. Acylated forms were also obtained in high abundance depending of the extraction method. An extract concentration range of 4.31 to 7.23 mg/mL inhibited by 50% the growth of untransformed cells NIH3T3. Antiproliferative effect on PC3, Caco2, HepG2 and MCF7 cancer cells of acidified extracts from hybrid blue maize was larger than the observed using non-acidified extracts. Among the nine compounds that were quantified in the extracts tested, CyMalGlu I showed the strongest correlation with the reduction of cell viability in Caco2 (-0.876), HepG2 (-0.813), MCF7 (-0.765) and PC3 (-0.894). No significant correlation or differences in antiproliferative effect on HT29 was found among the extracts. The method of extraction of maize anthocyanins must be selected to obtain a high yield of CyMalGlu I more than only Cy3-Glu since acylation affects the inhibition of cancer cell growth.