Knowledge of the effect of primary Sjögren's syndrome (pSS) on the microbial flora in the different predilection sites for oral disorders is needed for planning preventive treatment. We carried out microbial analysis of samples from the dorsum of the tongue, smooth mucosa, supragingival tooth surfaces, and the gingival crevice region of 20 patients with pSS. A clinical oral examination was performed and whole unstimulated and stimulated secretion rates were measured. Compared with healthy controls, subjects with pSS harbored higher numbers and frequencies of Streptococcus mutans, Lactobacillus spp., and Candida albicans in the supragingival plaque. On the smooth mucosa and tongue, the pSS subjects displayed an increased frequency of C. albicans, Staphylococcus aureus, enterics, and enterococci. C. albicans was detected about twice as frequently in the supragingival plaque as it was on the tongue. In the gingival crevice region, the pSS group harbored slightly lower proportions of Fusobacterium nucleatum and Prevotella intermedia/Prevotella nigrescens than controls. The clinical and microbial differences were mainly due to the pSS subjects with a stimulated secretion rate of < 0.5 ml/min. Porphyromonas gingivalis and Actinobacillus actinomycetemcomitans were not detected in any subject with pSS. The microbial flora in the different ecosystems reflected the status of oral disorders in the subjects with pSS. Specific site sampling and analysis in subjects with pSS revealed further differences compared with controls, and is therefore preferable to saliva sampling for oral treatment planning and for the evaluation of the effect of oral treatment and of preventive measures implemented in individuals with pSS.