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Dental caries is a biofilm-mediated, dynamic disease with early onset. A balanced salivary microbiota is a foundation of oral health, while dysbiosis causes tooth decay. We compared the saliva microbiota profiles in children with and without caries. The study consisted of 617 children aged 9-12 years from the Finnish Health in Teens (Fin-HIT) study with available register data on oral health. Caries status was summarised based on Decayed, Missing, and Filled Teeth (DMFT) index in permanent dentition. The children were then classified into the following two groups: DMFT value ≥ 1 was considered as cavitated caries lesions (hereafter called 'caries') (n = 208) and DMFT = 0 as 'cavity free' (n = 409). Bacterial 16S rRNA gene (V3-V4 regions) was amplified using PCR and sequenced by Illumina HiSeq. The mean age (SD) of the children was 11.7 (0.4) years and 56% were girls. The children had relatively good dental health with mean DMFT of 0.86 (1.97). Since sex was the key determinant of microbiota composition (p = 0.014), we focused on sex-stratified analysis. Alpha diversity indexes did not differ between caries and cavity free groups in either sexes (Shannon: p = 0.40 and 0.58; Inverse Simpson: p = 0.51 and 0.60, in boys and girls, respectively); neither did the composition differ between the groups (p = 0.070 for boys and p = 0.230 for girls). At the genus level, Paludibacter and Labrenzia had higher abundances in the caries group compared to cavity free group in both sexes (p < 0.001). Taken together, there were minor differences in saliva microbiota between children with and without caries. Potential biomarkers of caries were the sugar metabolisers Paludibacter and Labrenzia. These bacteria presumably enhance salivary acidification, which contributes to progression of dental caries. The clinical relevance of our findings warrants further studies.