We compared serological and clinical presentation of 38 adults (5 males, 33 females) and 37 children (15 boys, 22 girls) with anti-endomysial antibodies (AEA).AEA, antinuclear (ANA), anti-parietal (APA), anti-thyroid microsomal (ATMA), anti-thyreoglobulin (ATGA), anti-smooth muscle (SMA) and anti-mitochondrial (AMA) antibodies were detected by IIF. Anti-tissue transglutaminase (tTG), anti-extractable nuclear antigens (ENA) and anti-actin (AAA) antibodies were studied by ELISA. There were no differences in frequency of ANA, APA, ATGA, SMA, AMA and AAA in children and adults. ATMA (p < 0.001) and anti-ENA (p < 0.05) positivity were more frequently found in adults. Anti-Ro/SSA had 7/38 adults and 1/37 children (p < 0.05). Adults had more frequently silent form of celiac disease associated with autoimmune diseases (p < 0.001). We are the first to demonstrate that in spite of no difference in ANA positivity in adults and children, ANA in adults more frequently target ENA, especially Ro/SSA antigen. The reason for this ANA specificity could be the longer gluten exposure in adults.