The aim of our study was to determine the reproducibility of a new semi-quantitative scoring system based on ultrasonographic (US) evaluation of structural changes of salivary glands in primary Sjögren's syndrome (SS). US evaluation of parotid and submandibular glands was performed in 28 SS patients and 29 control subjects independently by two blinded observers. Echogenicity, delineation of glandular borders and sonographic structure (homogeneity, hypoechoic areas, hyperechoic foci) of salivary glands were semi-quantitatively assessed and the final US score calculated. Inter-observer variability was determined by Cohen's test. A high degree of inter-observer agreement was found regarding the final US score (0.90) and in the assessment of glandular homogeneity (0.90), echogenicity (0.88) and hypoechoic areas (0.88). This study showed good reproducibility of the US evaluation of salivary glands using our novel scoring system. This may have important implications on the diagnostic algorithm in patients with SS.