The native human saliva obtained through the centrifugation of whole saliva showed characteristic salivary protein complex (SPC) peaks in gel filtration high performance liquid chromatography (HPLC) using Superose 12 column1,2). In the previous study the SPC peaks in chromatography were explored to know their composition and functions by different detection methods, but still the nature of SPCs was not clearly elucidated so far. In this study the SPC peaks were examined by direct antibody interaction in order to target different antimicrobial and protective proteins distributed in the SPCs via gel filtration HPLC. As the SPC peak shape and migration speed can be changed by antibody binding to specific proteins of SPC, it was found that mucin1 is evenly distribution in all SPCs, while PRPs are more abundant in the late dominant SPC than the early dominant SPC and also in the intermediated SPCs. Most of antimicrobial proteins including lysozyme, LL-37, lactoferrin, β-defensin-1, -2, -3, IgA, mucocidin, and α1-antitrypsin were more abundant in the late dominant SPC than the early dominant SPC, while histatin showed relatively even distribution in all SPCs. Therefore, it was presumed that the late dominant SPC containing abundant antimicrobial and protective proteins could be applied as a biomarker to measure the defensive potential of whole saliva in oral diseases.