Objective: The objective of this study was to determine whether differences in the abundance of mucins 5b and 7 as well as secretory IgA exist in the oral acquired pellicle between children with active caries and caries-free children. Design: Pellicle formation was performed for 10 min in-situ on ceramic slabs in the oral cavity of children (5–7 years of age) with caries (n = 15) and without signs of caries (n = 13). Furthermore, unstimulated saliva was collected. Concentrations of Muc5b, Muc7 and sIgA were measured in desorbed pellicle eluates and in saliva. Results: Significantly larger concentrations of Muc5b, Muc7 and sIgA were detected in the pellicle obtained from children with caries compared to caries-free children. However, in the salivary samples concentrations of mucins Muc5b and Muc7 as well as sIgA did not differ significantly between the two groups. Conclusions: All three pellicle components Muc5b, Muc7 as well as sIgA could be identified as potential biomarkers for early childhood caries with high sensitivity and specificity. This could contribute to a better understanding of the different caries susceptibility in children.