AIMThis study aimed to evaluate salivary cytokine levels and the prevalence of cariogenic bacterial species in children with active dental caries compared to caries-free peers.METHODSThis cross-sectional study involved forty randomly selected children aged 7-9 years, who were divided into caries-active or caries-free groups. DNA was extracted from supragingival plaque using the DNeasy kit and analysed. Microbial profiling was conducted using HOMINGS 16S rRNA gene sequencing. Saliva samples were also collected and analysed using multiplex cytokine bead assays on the Luminex system to assess cytokine levels.RESULTSThe caries-active group exhibited significantly higher relative abundance of genera Leptotrichia, Veillonella, and Kingella (p < 0.05). At the species level, Streptococcus sanguinis, Leptotrichia shahii, Streptococcus mutans, Leptotrichia sp. HOT_498, TM7[G-1] sp. HOT_346, Rothia dentocariosa were significantly enriched in the caries-active group. In females, IL-15 and IL-1β were significantly elevated in the caries-active group, with no cytokine differences observed in males or overall levels. The relative abundance of Leptotrichia shahii, Streptococcus mutans, Streptococcus sanguinis, TM7[G-1] sp. HOT_346, Abiotrophia defectiva, and Rothia dentocariosa significantly correlated with cytokines, including Aggrecan, BAFF, CD-40L, IL-1β, IL-5, IL-8, IL-11, IL-15, IL-17, IL-23, IL-28A, MIP-3α, Pentraxin 3, and TNF-α. In the caries-free group, only Leptotrichia hongkongensis showed a significant association with IL-10.CONCLUSIONDistinct microbiome differences at both the genus and species levels were observed between caries-active and caries-free groups. Salivary cytokine levels were similar between the groups, except for higher IL-15 and IL-1β in females from the caries-active group. Correlations between bacteria and cytokines in the caries-active group highlight the need for further research on the microbiome-immune interaction in caries development.CLINICAL SIGNIFICANCEMicrobiome profiles, cytokine levels, and their potential correlation in caries-active children suggest that further study and understanding of these factors could help identify individuals at higher risk for caries and guide preventive care.