Objective To investigate the relationship between genotypic diversity of Streptococcus mutans(Sm)and deciduous teeth caries in Xinjiang Uygur autonomous region.Methods Isolates of Sm were obtained from 17 caries-free and 17 caries-active Uygur preschool children aged from 3 to 5 years.A total of 143 isolates were subcultured,biochemically characterised and identified by polymerase chain reaction(PCR)as Sm and Streptococcus sobrinus(Ss).Then the Sm isolates were genotyped by arbitrarily primed-PCR(AP-PCR).Results A total of 81 Sm isolates from caries-active subjects and 62 isolates from caries-free subjects were identified by PCR and forty distinct genotypes identified from 143 clinicalisolates.In seventeen caries-active group,9 children had only 1 genotype,5 children had 2 genotypes,3 children had 3 genotypes.In seventeen caries-free group,14 children had only 1 genotype,3 children had more than 2 genotypes.The Spearman correlation test showed a strong associatiou between genotypic diversity and caries experience(r=0.342.P<0.05).Conclusions Isolates of Sm in caries-active Uygur preschool children show apparent more genetic diversity than those in caries-free children.The genotypes of isolates might be related to differences in caries susceptibility.