In order to know the characteristic roles of salivary protein complex (SPC) the gel-filtration chromatography was performed using the unstimulated and the stimulated whole saliva separately. The first and second dominant SPC peaks were fractionated and analyzed by immunoprecipitation HPLC (IP-HPLC) using antibodies against the essential salivary proteins including α-amylase, mucin-1, proline rich proteins (PRPs), histatin, cystatin, LL-37, lysozyme, lactoferrin, -defensin-1, -2, -3, IgA, transglutaminase 4 (TGase 4), mucocidin, α1-antitrypsin, cathepsin G. In the gel-filtration chromatography the stimulated whole saliva showed much reduced amount of SPCs than the unstimulated whole saliva, but the proportional patterns of both whole saliva were almost similar each other. Through IP-HPLC analysis both of the first and second dominant SPCs were variably positive for the essential salivary proteins, however, α-amylase, mucin-1, PRPs, lysozyme, and cathepsin G were predominant in the first dominant SPC, while cystatin, lactoferrin, β-defensin-1, -2, -3, IgA, mucocidin, TGase 4, and α1-antitrypsin were predominant in the second dominant SPC. And more, the α1-antitrypsin and cathepsin G which were mostly derived from gingival crevicular fluid were also consistently found in the SPCs. These data may suggest that the first dominant SPC, rich in α-amylase, mucin-1, PRPs, lysozyme, and cathepsin G, may play a role in food digestion, protein degradation, and mucosa lubrication, while the second dominant SPC, rich in cystatin, lactoferrin, β-defensin-1, -2, -3, mucocidin, IgA, TGase 4, and α1-antitrypsin, may play a role in the mucosa protection and antimicrobial defense.