Enterovirus 71 (EV71) is the most common aetiological agent detected in cases of hand, foot and mouth disease (HFMD) resulting in incidences of neurological complications and fatality in recent years. A comparison of the capsid proteins implicated in the pathogenicity of the fatal and non-fatal strains of EV71, reveals a high degree of homology (93%-100% identity). To facilitate diagnostic immunoassays and vaccine development, a consensus structural model for the EV71 coat protein has been developed based primarily on the homologous structure of the bovine enterovirus. The overall architecture of the virion closely resembles those of related icosahedral picornaviruses. Detailed atomic modelling of the fatal 5865/SIN/00009 strain has been carried out, and the functional regions (known and predicted) from closely related viruses mapped onto the surface of the predicted structure. From the model, we have identified two putative immunogenic regions, one of which is unique to EV71. The hydrophobic pocket within VP1, found in bovine enterovirus, poliovirus and rhinovirus, is also conserved in EV71.