To find an association between oral mucosal human papilloma- and/or Epstein-Barr (HPV, EBV) virus infection in patients with dry mouth and/or Sjögren's syndrome (SS) compared to healthy controls and to find connections with salivary gland histopathological alterations. Ninety-two participants were divided into four groups: 1. healthy controls (n = 32); 2. xerostomia (n = 28); 3. hyposalivation (n = 22); and 4. SS groups (n = 10). To detect virus infection brush biopsy was outlined in all groups. Detections of virus-specific sequences were achieved with polymerase chain reaction (PCR). Lip biopsy and histopathological assessment was performed in groups 2, 3 and 4. HPV positivity of oral mucosal cells was shown in group 1: 1 (3.12%); group 2: 3 (10.7%); group 3: 2 (8.26%); and in group 4: 0 of the samples. EBV was present in group 1: 14 (43.7%); group 2: 17 (60.7%); group 3: 6 (27.3%); and in group 4: 5 (50%) of the cases. There was no statistically significant difference between the attributes. Intact salivary gland in 28.2%, chronic sialadenitis in 28.2%, stromal fibrosis in 6.5%, lipomatous atrophy in 8.6%, fibrous atrophy in 6.5% and positive focus score (SS) in 26.1% were found in the subjects. Neither HPV nor EBV infection caused statistically significantly more histological abnormalities. Orofacial mucosal HPV and/or EBV DNA rates did not differ statistically significantly in patients with xerostomia or hyposalivation or SS compared to healthy controls, therefore, it cannot prove the provocative role of these viruses in dry mouth and/or SS. Neither dry mouth nor SS were accompanied by statistically significantly more salivary gland alterations in HPV- and/or EBV-positive subjects; these alterations are frequent in the virus-negative cases too.