Abstract. Sjögren syndrome (SS) is characterized by dysfunction of the exocrine glands, particularly the salivary and lacrimal glands. Thus, labial salivary gland biopsy is useful method for diagnosing SS. The aim of the present study was to investigate the microRNA (miRNA or miR) profile of labial salivary glands obtained from SS patients and to examine the correlation of miR-181a and -16 levels with the pathological grade in SS. miRNA expression in labial salivary gland tissues was profiled in 3 female patients with primary SS and 3 female patients with non-SS sicca syndrome using microarray analysis. In addition, a literature search and miRNA target gene prediction were performed to collect miRNAs involved in SS pathogenesis. Subsequent to integrating all database results, miR-181a and -16 were identified to be associated with the Ro/SS-associated antigen A and La/SS-associated antigen B during SS pathogenesis. Therefore, these miRNAs were selected for further verification in labial salivary gland tissues of 28 patients with SS and 18 non-SS sicca syndrome control individuals by quantitative reverse transcription-quantitative polymerase chain reaction. Compared with the control group, 76 miRNAs were upregulated and 51 were downregulated in the labial salivary gland of SS patients according to microarray results. In particular, miR-181a and -16 expression levels in the labial salivary gland of SS patients were decreased in comparison with those in the controls. Furthermore, the decreased expression levels of these miRNAs were associated with the labial salivary pathological focus scores. In conclusion, the present study examined the miRNA profiles in the labial salivary glands of SS patients and detected decreased miR-181a and -16 expression levels compared with the control individuals. Finally, the decreased levels of miR-181a and -16 were associated with the salivary gland pathological focus scores, suggesting that miR-181a and -16 may serve a role in the pathogenesis of SS.