A study was performed to investigate whether expression of aquaporin (AQP) 3 and 5 has potential as a marker for distinguishing dry mouth from Sjögren’s syndrome. Twenty-five patients underwent labial minor salivary gland biopsy (dry mouth, n = 9; Sjögren’s syndrome, n = 16; control, n = 8). All patients were interviewed about their medical history and subjective oral symptoms, and intraoral examinations were conducted. Quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry were used to examine the expression and localization of AQP3 and 5. Significant differences in oral dryness, dry eye, medical history, and Saxon test results were revealed among the groups. However, there were no significant inter-group differences in expression of mRNA for AQP3 and 5. Immunohistochemical staining for AQP3 was localized mainly in the basolateral and part of the ductal cell membrane, and was barely evident in the apical membrane of acinar cells. AQP5 was localized to the basolateral and apical membrane and cytoplasm, but not the ductal cell membrane. Staining intensity for AQP3 in the apical membrane was significantly stronger in Sjögren’s syndrome, and that for AQP5 was significantly weaker in dry mouth. Taken together, the present data suggest that expression of AQP3 and 5 may be a marker for distinguishing between patients with dry mouth and those with Sjögren’s syndrome.