This study determined the frequency with which 38 microbial species were detected in 171 randomly selected children from 6 to 36 months of age. Children were sampled and dental caries measured. Oral samples were assayed by means of a checkerboard DNA probe assay. The detection frequencies from tongue samples in children under 18 mos were: S. mutans 70%, S. sobrinus 72%, P. gingivalis 23%, B. forsythus 11%, and A. actinomycetemcomitans 30%, with similar detection frequencies in children over 18 mos. Thus, S. mutans and the periodontal pathogens, P. gingivalis and B. forsythus, were detected even in the youngest subjects. Species associated with caries included S. mutans (children ages 18-36 mos) and A. israelii (children ages < 18 mos), the latter species possibly reflecting increased plaque in children with caries. Species detection from tooth and tongue samples was highly associated, with most species detected more frequently from tongue than from tooth samples in children under 18 mos, suggesting that the tongue was a potential microbial reservoir.