The aim of this study was to investigate the microbiota of noncaries associated supra-gingival plaque (SGP) microbiology in Sjögren's syndrome (SS). Stimulated whole saliva (SWS) and full-mouth SGP on intact tooth surfaces were collected from 26 primary (p) SS, 27 secondary (s) SS, and 29 control subjects for selective culture of lactobacilli, mutans streptococci, and aerobic and facultatively anaerobic gram-negative rods (AGNR). Predominant cultivable anaerobes from SGP of 11 randomly selected subjects from each group were investigated. Clinical and sialometric data were also collected. SS sufferers had significantly lower SWS flow rate and higher mean DMFT (decayed, missing, filled teeth), while pSS subjects also had lower SWS pH and fewer standing teeth. Lactobacillus acidophilus levels in SWS (P = 0.012) and SGP (P < 0.0001) were significantly elevated in pSS sufferers compared with sSS individuals and controls. AGNR isolation was uncommon. SS sufferers had significantly lower proportion of gram-negative species (P = 0.047). Non-oral species were isolated in greater proportions from pSS SGP (P = 0.007). Subjects with pSS harbored increased levels of L. acidophilus and non-oral species, while SS sufferers generally had lower proportions of gram-negative species. The microbial composition of noncaries associated SGP indicates a potential source of increased caries risk in SS.