Although prolonged bottle feeding with a carbohydrate-rich content is commonly agreed to be the main etiologic factor for early childhood caries (ECC), in recent years additional endogenous factors, including the composition of saliva, have been suspected as predisposing factors in children for the development of this aggressive form of dental caries. As a basis for investigating the putative involvement of salivary proteins in the etiology of ECC, a qualitative comparison of major salivary protein profiles between children with ECC and caries-free controls was performed. Saliva was collected from 30 children with ECC and, after separation by sodium dodecyl sulphate–polyacrylamide gel electrophoresis, was compared with saliva from 20 caries-free controls for the general composition of proteins by means of silver staining, glycoprotein staining, and lectin blotting. Gels and blots were analysed using densitometry, and the protein-banding patterns resulting from the individuals’ samples were compared by image analysis for the presence or absence of protein bands. Dendrograms obtained after comparison of all samples showed a high degree of similarity for the experimental groups. In summary, the results attest a uniform expression of the major protein components in children’s saliva, regardless of the clinical manifestation of ECC, and thus pave the way for further detailed investigations of more subtle differences in the salivary proteome.