The goals of this cross-sectional study were to characterize and compare demographic, behavioral, and environmental factors potentially associated with early childhood caries (ECC) and to assess salivary levels of mutans streptococci (MS) and lactobacilli (LB) in underserved, predominantly Hispanic children. One hundred forty-six children aged 3 to 55 months with a range of caries experience were identified and examined. ECC was primarily associated with the presence of MS and lack of access to dental care. Salivary MS levels among young children with ECC were higher than would be expected in a dentally healthy population, but lower than levels reported among older children at high risk for caries. After adjustment for age, children with log10 MS > or = 3.0 or log10 LB > or = 1.5 were about five times as likely (OR=4.9, 95% CI=2.0, 12.0) to have ECC than those with lower bacterial levels. This study demonstrated a significant association between relatively low cariogenic bacterial levels and dental caries in infants and toddlers. Antibiotic use, exposure to lead, and anemia were not significantly associated with the number of decayed and filled surfaces or decayed and filled teeth. ECC correlated significantly with child's age and lack of dental insurance of the children, as well as inversely with both family income and the educational level of the mother of the child.