Objective:  To investigate the salivary protein profile in patients with Sjögren’s syndrome (SS), and healthy control subjects.

Materials and methods:  Unstimulated whole saliva samples were collected from 16 age‐matched females; eight healthy subjects and eight patients diagnosed with SS (six primary SS, one incomplete SS and one primary SS associated with B cell lymphoma). Proteins were extracted and separated individually by 2D sodium dodecyl sulphate–polyacrylamide gel electrophoresis. Selected protein spots of interest were analysed by electrospray ionization – tandem mass spectrometry. Obtained data were searched against the Swiss‐Prot and NCBI non‐redundant protein databases using Mascot software.

Results:  Two groups of patterns of protein expression were observed in the eight SS patients: a major group (six patients) with significant expression differences from the healthy subjects and the second group (two patients) with a pattern similar to the eight healthy subjects.

Conclusion:  In this preliminary study, protein expression differences were found between SS patients and healthy subjects. Individual analysis of SS patients exhibited two patterns of protein expression with no direct relation to the clinical, serological or histological severity of disease. This study emphasizes the difficulty of the present proteomic knowledge to diagnose and monitor the sequel of SS development.