Mutans streptococci (MS) and lactobacillus (LB) counts (CRT Bacteria chair-side test) were compared and correlated with the respective caries experience (DMF) of cystic fibrosis (CF) homozygotes (n = 20), CF heterozygotes (n = 20) and healthy controls (n = 20). Each group of subjects was divided into two equal age groups: group A <20 years and group B >20 years. No significant differences were found regarding DMF between the three groups. CF heterozygotes had a significantly higher DMF-S than CF homozygotes (p = 0.040). This was also found in age group B (p<0.02), where it also counted for DMF-T (p<0.01). When in age group B, CF heterozygotes and controls were combined as one group, it was found that they had a significantly higher DMF-T (p = 0.031) and DMF-S (p = 0.008) than CF homozygotes. No significant differences in LB counts between the three groups were observed. CF homozygotes and those in age group A had significantly (p = 0.018 and p = 0.015) more low MS counts. LB and MS counts were positive and significantly correlated with DMF-T/-S in CF homozygotes and in the combined group of CF heterozygotes with controls (p< or = 0.05 and < or = 0.001). No correlations between bacterial counts and DMF were observed in CF heterozygotes. It can be concluded that despite the fact that CF homozygotes behave as high caries risk individuals, they did not have significantly more dental decay. More research is required in order to explore salivary, dietary and medication influences.