Aim: To compare the salivary microbial profile in children with oral clefts to matched non-cleft controls in a cross-sectional study.

Methods: The cleft group consisted of 80 children aged 5 years and 144 age-matched non-cleft children were recruited as a control group. Stimulated whole saliva samples were collected and analysed with checkerboard DNA–DNA hybridisation using 12 pre-determined bacterial probes. Background data on caries, oral hygiene, dietary habits and fluoride exposure were collected from clinical examinations and questionnaires.

Results: Children in the cleft group had a significantly higher prevalence of dental caries but only minor differences in the salivary microbial profile were found. In general, the cleft-children displayed a lower prevalence of common commensal species (e.g. Streptococcus, Fusobacterium) when compared with the non-cleft controls. The differences were statistically significant (p < 0.05) but the clinical significance was unclear.

Conclusions: The profile of the salivary microflora in 5-year-old children with and without oral clefts was basically similar and displayed only marginal differences with respect to commensal bacteria.