Autoantibodies against the transcriptional DEK protein have been considered characteristic of the pauciarticular onset subtype of juvenile rheumatoid arthritis (JRA) associated with iridocyclitis in young girls. In this study we investigated the presence of anti-DEK autoantibodies in the sera of 288 patients with SLE using a recombinant DEK protein as autoantigenic target. Thirty sera (10.4%) were positive against DEK protein by immunoblotting. Patients with anti-DEK autoantibodies show a lower frequency of cutaneous manifestation, exhibit more frequently certain markers of a chronic inflammatory status like anaemia and positivity for C-reactive protein, as well as a higher frequency of anti-double-stranded DNA autoantibodies. In contrast to JRA patients positive for anti-DEK autoantibodies, no association with erosive arthritis nor iridocyclitis were found in SLE. In conclusion, our results show that 10.4% of SLE patients from our area show antibodies against DEK protein, although this feature did not clearly establish a clinical subset of the disease.