A variety of proteins produced by Streptococcus pyogenes contribute to the virulence of the pathogen. Among the proteins; the M protein and streptococcal pyrogenic exotoxins (Spe) are considered the major S. pyogenes virulence factors. To better characterize the correlation of M protein type and pyrogenic exotoxins with clinical diseases, we tested 269 S. pyogenes clinical isolates from patients with scarlet fever, pharyngitis, skin infection, otitis media, or other invasive streptococcal infections that provided appropriate clinical data. The strains were genotyped (M type) and assayed for speA, speB, and speC genes. The speB gene was detected in all isolates. Also, speA and speC genes were detected in 54 strains (18.2%) and 140 strains (47.3%), respectively. The strains isolated from invasive disease patients showed the highest frequency of speA gene (40.5%). The correlation among emm genotype, speA gene, and clinical patterns was analyzed. Genotypes emm1 (55.6%) and emm3 (22.2%) were predominant in stains with speA gene. The distribution of emm genotypes did not significantly associate with clinical patterns. These data suggest that SpeA is significantly associated with specific emm genotypes, and the exotoxin serve a dominant virulence factor.