Objective To study the prevalence of superantigens, deoxy ribonuclease(DNase) genes and fibronectin-binding protein encoding (FBP) genes of Group A Streptococci(GAS) isolated from children, and to analyze its relationship with clinical infections and predominant emm type. Methods A total of 112 strains of GAS were collected from three Children's Hospitals during the period from 2008 to 2012, including 72 strains from patients and 40 strains from asymptomatic carriers.Emm, superantigens(speA, speC, speH, speI, speG, speJ, ssa, smeZ, speL, speM, speK and speF), DNase genes (sda, sdn, spd1, spd3 and spd4), phospholipase A2 gene and FBP genes (prtFl、prtF2、fba) were amplified by PCR, and emm was further typed by DNA sequencing. Results A total 7 types were identified, including emm1, emm12, emm22, emm4, emm77, emm86, and stG485.The most common emm type was emm12, which accounted for 68.8% of all isolates in this study.The emm type distribution of the pathogens was accorded with the carrier strains.The prevalence of 12 superantigens, including speA, speC, speF, speG, speH, speI, speJ, speK, speL, speM, ssa, smeZ were 13.4%, 95.5%, 85.7%, 74.1%, 63.4%, 63.4%, 14.3%, 0.9%, 0.9%, 0.9%, 74.1% and 93.8%, respectively.The prevalence of 5 DNase genes, including sda, sdn, spd1, spd3, spd4, was 66.96%, 12.5%, 94.64%, 27.68%, 0.89%, respectively.No sla gene was detected.The prevalence of fibronectin-binding protein, including prtF1, prtF2, fba, was 69.6%, 79.5%, 30.4%, respectively.The carriage rate of speJ, spd3 from invasive or noninvasive infections was higher than that from asymptomatic carriers, however, the positive rate of ssa, speF, speG, prtF1, prtF2 and prtF1/prtF2 was lower than that of asymptomatic carriers.The prevalence of speH, speI, speG, sda, spd1, prtF1, prtF2, prtF1/prtF2 from the emm12 isolates was higher than that from non-emm12 isolates, whereas speA, speJ, sdn, spd3 and fba were more common in non-emm12 isolates. Conclusions Emm12 is the prevalent genotype among S. pyogenes strains isolated from children, followed by emm1 and emm12, which is irrelevant to resources; Strains isolated from infected children and from asymptomatic carriers have different distribution characteristics of virulence genes; The prevalence of emm12 may be associated with the high carrier rate of the certain virulence gene. Key words: Streptococcus pyogenes; Virulence factors; Emm typing