The characteristics of 359 group A streptococcal (GAS) isolates collected from Chinese paediatric patients in two periods (1993-1994, 2005-2006) were studied. Isolates were assigned to emm types and assayed for eight superantigen (SAg) genes (speA, speC, speH, speI, speG, speJ, ssa, SMEZ). Types emm1 and emm12 were consistently the most prevalent during the two periods, while others varied in frequency. GAS isolates carrying six or more SAg genes increased from 46.53% (1993-1994) to 78.39% (2005-2006); ssa, speH and speJ genes (P<0.05) increased but speA declined (P<0.05). SAg gene profiles were closely associated with the emm type, but strains of the same emm type sometimes carried different SAg genes in the two periods. No significant difference in emm-type distribution and SAg gene profile was noted between isolates from different diseases. These data may contribute towards the development of a GAS vaccine in China.