Group A streptococcus (GAS) is a human obligate pathogen whose arsenal of virulence factors result in a diversity of disease. The genetic differences in GAS that underpin association with these different diseases have not been full elucidated. Although both the presence and absence of specific virulence genes, and their expression profiles are likely to be important in disease outcome, genetic analysis of the latter has not been studies in detail. Here we conducted a comparative genetic study of the 500 base pairs upstream of 14 regulatory two-component systems (TCS) present in 52 GAS genomes. We report that not all TCS are present in all genomes, and that truncations, likely to result in loss of function of TCS activity were also observed. More specifically, all M89 and M53 GAS isolates tested lacked genes from the spy1107 and salK loci, respectively. The genetic variation in these regions included both SNPs and indels. Recombination was also evident in the mga locus. While allelic variation of each TCS untranslated region (UTR) was conserved within emm-types, individual alleles could also be present in multiple emm-types. When compared with disease, specific sptR UTR alleles where associated either with nephritogenic- or rheumatogenic- associated isolates. Variation displayed in the upstream alleles of the TCS of M89 isolates promises to inform the variable virulence and evolutionary history of epidemic isolate clades. These results suggest that variation in the UTR of TCS may be markers, or even contribute to specific diseases.