Systemic onset JIA is dramatically different from the other forms of JIA clinically. While HLA associations are a significant genetic factor in most of the JIA subtypes, there are few or no associations with systemic JIA. We studied the frequencies of class I and II antigens in 47 Polish patients (8-35 years old) with systemic onset JIA. The mean age of onset was 4.5±3 years (range 7 months – 11 years). The mean disease duration was 18±7.4 years. When the antigen frequencies for JIA patients were compared to a normal control population, significantly higher frequencies of B27, DR4 and DR3 antigens were found, while the frequencies of DR6 were lower. This study confirms previous reports of an increased incidence of DR4 and HLA B27 in these patients and suggests an association of DR3 with systemic onset JIA in the Polish population.