Coxsackievirus A16 (CA16) and enterovirus 71 (EV71) are known to be major causative agents of hand-foot-and-mouth disease prevalent in summer in Japan. Discrimination and identification of these viruses were often hampered by a nonneutralizable or nontypable virus. Therefore, a Southern blot hybridization that utilizes mixed probes specific to serotype was developed. Firstly, an approximately 650 bases spanning 5'-noncoding region to one third of VP2 including entire VP4 was amplified with a set of primers containing enterovirus common sequences and a genomic RNA as template. Secondary, the nucleotide sequences were determined using seven CA16 and eighteen EV71 strains including the standard strains, and the deduced amino acid sequences of VP4 were searched to find residues which are conserved in the same serotypes but diverged among different serotypes. Candidate positions for the mixed probes were defined at the carboxyl terminus of VP4. Thirdly, Southern blot analyses were carried out using thirty-nine enterovirus standard strains, seven CA16 isolates and sixty-six EV71 isolates previously identified by the neutralization test. The results revealed that each mixed probe exclusively bound to the homologous DNAs but not to the heterologous ones. In an attempt to determine serotypes without virus isolation, clinical specimens from hand-foot-and-mouth disease were examined. Of 78 throat swabs and 15 vesicular fluids, 71 (91.0%) and 13 (86.7%) specimens were clearly identified, indicating that the method described here offer advantages over the traditional neutralization assay: It is rapid, specific and less labor-consuming.