Previous cross-sectional studies using bacteriocin profiles, serotyping, or genotyping suggest that mothers are the principle source of mutans streptococci (MS) to their infants. This study determined the commonality of MS genotypes between mothers and their infants at the time of initial acquisition. Oral bacteria of mothers and their infants were monitored from birth for approximately 3 years at three-month intervals. Genotypes of MS in infants appeared identical to those present in mothers in approximately 71% of 34 mother-infant pairs studied. Interestingly, female infants acquired MS genotypes identical to their mothers' with significantly greater fidelity than male infants (88% vs. 53%). Homology of genotypes between mothers and their infants at initial acquisition strongly suggests that MS strains were transmitted from mother to infant and that this transfer exhibited gender specificity. In no instance did we observe homology of genotypes between fathers and infants or fathers and mothers, further supporting the notion that acquisition of MS in humans follows maternal lines. Although the prevalence of dental caries was low in this young child population (11/34; 32%), we observed that male children who harbored the same genotype as their mothers had a 13 times greater likelihood of having caries than female children who acquired their mothers' strain; this difference was statistically significant (p < 0.01). Although we do not know the biological mechanisms governing fidelity of acquisition between a mother and her infant, our data suggest that caries outcome may be, in part, determined by both the source of MS and the presence of a specific genotype of MS.(ABSTRACT TRUNCATED AT 250 WORDS)