OBJECTIVE: Primary Sjögren's syndrome (pSS) is a systemic autoimmune disease, and its pathogenetic mechanism is far from being understood. In this study, we aimed to explore the cellular and molecular mechanisms that lead to pathogenesis of this disease. METHODS: We applied single-cell RNA sequencing (scRNA-seq) to 57,288 peripheral blood mononuclear cells (PBMCs) from five patients with pSS and five healthy controls. The immune cell subsets and susceptibility genes involved in the pathogenesis of pSS were analyzed. Flow cytometry was preformed to verify the result of scRNA-seq. RESULTS: We identified two subpopulations significantly expand in pSS patients. The one highly expressing cytotoxicity genes is named as CD4 CTLs cytotoxic T lymphocyte, and another highly expressing T cell receptor (TCR) variable gene is named as CD4 TRAV13-2+ T cell. Flow cytometry results showed the percentages of CD4 CTLs, which were profiled with CD4 and GZMB staining; the total T cells of 10 patients with pSS were significantly higher than those of 10 healthy controls (= 0.008). The expression level of IL-1β in macrophages, TCL1A in B cells, as well as interferon (IFN) response genes in most cell subsets was upregulated in the patients with pSS. Susceptibility genes including HLA-DRB5, CTLA4, and AQP3 were highly expressed in patients with pSS. CONCLUSIONS: Our data revealed disease-specific immune cell subsets and provided some potential new targets of pSS. Specific expansion of CD4 CTLs may be involved in the pathogenesis of pSS, which might give valuable insights for therapeutic interventions of pSS.