BACKGROUND Investigation of morphological differences in relation with serological variables between primary versus secondary Sjögren's syndrome associated with systemic scleroderma (Scl-SS). METHODS A total of 69 primary Sjögren's syndrome (pSS) and Scl-SS patients were grouped according to the American-European Consensus Group criteria. Serum autoantibody information was obtained from the patient records. Hematoxylin and eosin sections of the minor salivary gland biopsy were reevaluated, and the lymphocyte focus score (FS), plasma cell focus, and fibrosis rates were all evaluated. RESULTS There were 43 pSS and 26 Scl-SS cases. Both biopsy and autoantibody were positive in 16 pSS cases while only biopsy was positive in 25 cases and only antibody in 1 case. Both biopsy and antibody were positive in 5 Scl-SS cases while only biopsy was positive in 18 and only antibody in 3 cases. The plasma cell focus was statistically significantly higher in pSS cases (P = 0.003). No difference was seen between Sjögren' syndrome (SS) subtypes in terms of lymphocyte FS, fibrosis, and autoantibody positivity. CONCLUSIONS We found that plasma cell focuses could be found more frequently in pSS than Scl-SS. In addition, our study reveals that the coexistence of SS and systemic scleroderma decreases the incidence of FS value ≥1 compared to pSS.