As the human mixed saliva plays important roles for the protection, regeneration, immunity, and molecular transfer/ signaling in the oral and gastro-intestinal mucosa, the salivary contents have great implications for the general health of human body. Nevertheless, the analysis method of human saliva has not been well developed up to date, because the proteins of mixed saliva are rapidly interacted with each other and easily degraded by proteolytic enzymes and microorganisms. This study aims to develop an immunoprecipitation-based high performance liquid chromatography (IP-HPLC) for the analysis of human mixed saliva. The representative IP-HPLC analyses were performed to compare among different subjects in variable general conditions. Compared to the normal control the subjects suffered from bacterial infections of gastro-intestinal enteritis, chronic periodontitis, and acute necrotizing gingivo-stomatitis showed dramatic increase of LL-37 level depending on the severity of diseases, while the subject suffered from Herpes stomatitis, a viral infection showed great increase of β-defensin 2. These data indicate that LL-37 in human mixed saliva is more responsible to the bacterial infections of gastro-intestinal enteritis, chronic periodontitis, and acute necrotizing gingivo-stomatitis, while β-defensin 2 is more responsible to the viral infection of Herpes stomatitis. This study also suggeststhat the IP-HPLC be easily applicable to the wide range of biological samples for the quantitative analysis of an objective protein.