Recent clusters of patients with acute rheumatic fever and invasive group A Streptococcus (GAS) have stimulated renewed interest in the epidemiology of streptococcal infections. We compared conventional serotyping for M and T antigens and serum opacity factor with field inversion gel electrophoresis (FIGE) for distinguishing among GAS. Fifteen pairs of throat isolates obtained from children positive for GAS before and after therapy were evaluated by conventional serotyping and by FIGE after SmaI digestion. Ten of the 15 pairs were identical by serotyping. FIGE correctly identified the 10 concordant and 5 discordant pairs. Individual clones were identified within each M type tested, including analysis performed on additional isolates of M1 and M3 obtained from the Centers for Disease Control and Prevention. This preliminary experience suggests that FIGE can successfully determine whether serial isolates from a given patient represent persistence of one strain or acquisition of a new strain of GAS and that this method might provide an alternative typing system for GAS.