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Effective caries control and management requires identification of susceptible children for timely intervention. Streptococcus mutans (S. mutans) is an important biomarker of caries risk.This study aimed to comparatively evaluate the validities of a novel immunoassay and a conventional culture-based assay in detecting salivary S. mutans in a paediatric cohort.190 children aged 3–4 years were recruited. The abundance of S. mutans in their saliva samples was analysed with three assay systems viz. a conventional culture-based assay (Dentocult SM), a novel immunoassay system (Saliva-Check MUTANS) based on monoclonal antibody technology and a Taqman real-time PCR assay taken as a gold standard.The novel immunoassay accurately differentiated saliva samples with high (≥5 × 105 CFU/mL) and low (<5 × 105 CFU/mL) S. mutans levels. The sensitivity/specificity was 97.6%/90.6%. The conventional culture-based assay reached a reasonably high sensitivity/specificity (92.8%/81.3%) in identifying children with moderate (≥104 CFU/mL) S. mutans level. Its sensitivity/ specificity in selecting children with high (≥105 CFU/mL) and very high (>106 CFU/mL) S. mutans levels were not sufficient (78.7%/79.8% and 25.8%/91.8%, respectively).The monoclonal antibody-based immunoassay accurately and rapidly determines S. mutans abundance in saliva and could be useful for chairside assessment of children's caries risk.