The anthocyanin content and antioxidant activity of kernels from 12 genotypes of waxy corn at two maturation stages (milk and mature) were investigated. The individual anthocyanins contained in coloured waxy corn were identified and quantified by HPLC-DAD-ESI/MS analysis. Cyanidin-3-glucoside and its derivatives were detected as being most dominant. Furthermore, acylated anthocyanins constituted 67.1–88.2% and 46.2–83.6% of the total contents at the milk and mature stages, respectively. The concentration of monomeric anthocyanin increased throughout the development of each genotype of corn. The antioxidant activity, which was determined by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging ability, increased with ripening. However, the ferric reducing antioxidant power (FRAP) and Trolox equivalent antioxidant capacity (TEAC) revealed decreases in some genotypes during ripening. The kernels of a purplish black waxy corn genotype (KKU-WX111031) exhibited the greatest antioxidant activity and contained the highest level of anthocyanins among the genotypes tested at both maturation stages.