A 3-year cohort study was carried out in 252 pre-school children for early identification of caries-active individuals. During this period information was collected about the acquisition of mutants streptococci and lactobacilli from the age of 2 till 5 years old. At baseline mutants streptococci were detected in 43% of the children while the detection frequency of lactobacilli was low (11.5%). On an individual level, numbers of colony-forming units of mutans streptococci and lactobacilli in plaque and saliva varied largely during the study period. The correlations between the numbers of lactobacilli and mutants streptococci in the saliva of the mother and the saliva and plaque of the child were low and never exceeded r = 0.22. Very low correlations (< r = 0.22) were also found between the numbers of mutans streptococci or lactobacilli and the diet in terms of the number of sugar intakes. Nevertheless, in children older than 2.5 years correlations between the clinical caries score and lactobacilli in saliva (range 0.31-0.62) and mutans streptococci in plaque or saliva (range 0.24-0.46) were highly significant (p < 0.01).