The aim of this study was to analyze the prevalence and clinical significance of circulating auto-antibodies against nuclear and non-nuclear antigens in a large cohort of Spanish patients with primary Sjögren's syndrome (SS). We studied 335 patients diagnosed with primary SS seen consecutively in our department since 1994 and tested for anti-nuclear antibodies (ANA), anti-Ro/SS-A, anti-La/SS-B, anti-Sm, anti-ribonucleoprotein (anti-RNP), anti-smooth muscle antibodies (anti-SMA), anti-parietal cell antibodies (anti-PCA), anti-liver-kidney microsome type-1 (anti-LKM-1) antibodies and anti-mitochondrial antibodies (AMA). ANA were detected in 278 (83%) patients. The association of positive ANA with the presence of anti-Ro/SS-A and anti-La/SS-B antibodies reached statistical significance at a titre of ANA >1/80 (p<0.001), while the presence of anti-Sm and anti-RNP was associated with positive ANA at a titre > or =1/320 (p=0.037 for Sm and p=0.016 for RNP). ANA titres correlated with the number of positive antibodies against specific nuclear antigens (p<0.001) but not with the number of positive antibodies against non-nuclear antigens. We found positive anti-Ro/SS-A antibodies in 111 (33%) patients, anti-La/SS-B in 78 (23%), anti-RNP in 8 (2%) and anti-Sm in 4 (1%). Anti-SMA antibodies were detected in 208 (62%) patients, with no significant associations with clinical or analytical SS features, while anti-PCA antibodies were found in 90 (27%) patients and were associated with a higher prevalence of thyroiditis and liver involvement. AMA were detected in 28 (8%) patients, although only 14 presented clinical and/or analytical evidence of liver involvement. No patient presented anti-LKM antibodies. ANA play a central role in the immunological expression of primary SS, due to their frequency and close association with the underlying presence of one or more anti-ENA antibodies. Positivity for antibodies against non-nuclear antigens such as anti-PCA and AMA suggests an association with some organ-specific autoimmune diseases (thyroiditis and primary biliary cirrhosis), while the presence of anti-SMA, in spite of their high prevalence, has no clinical significance in primary SS.