The protein components of saliva reflect the condition of the whole body as well as the salivary glands. The aim of this study is to characterize the gene expression profiles in each of the rat major salivary glands-the parotid, submandibular, and sublingual glands. Gene expression was analyzed using DNA microarrays, and observed differences in expression of representative genes were confirmed by quantitative, real-time polymerase chain reaction. Among the glands, the contribution to the high expression of genes encoding various proteins, specifically mucin 10, proline-rich glycoproteins, proline-rich protein 2, proline-rich proteoglycans, cystatin 10, amylase, deoxyribonuclease I, and von Ebner's gland protein, was significantly greater in the parotid gland than the other glands. The submandibular and sublingual glands had similar gene expression profiles that differed from profile of the parotid gland. For example, the genes encoding mucin 19 and ovomacroglobulin were highly expressed only in the submandibular and sublingual glands. In summary, we characterized gene expression in the rat major salivary glands and provided basic information on salivary gland marker proteins.