Enterovirus 71 (EV71) is one of the major causative agents of hand, foot and mouth disease. Recently, several EV71 inactivated vaccine candidates have been development in mainland China. To compare the antigenicity and genetic characteristics of different candidate vaccine strains for EV71, the genomes of 11 EV71 strains were sequenced. The cross-protection capacities were determined by neutralizing antibody test and were further assessed in neonatal mice. The results showed 93.0%-99.8% genome homology of the VP1 regions, but their cross-neutralization capacities varied. These results showed that vaccine strains with good cross-neutralization capacities had the potential to be vaccine strains.