Juvenile idiopathic arthritis (JIA) is the most common chronic arthropathy in childhood. Immune and genetic factors take part in the development of JIA and influence its consequence. Studies have identified association between JIA and genes encoding the human leukocyte antigens (HLA) . In this article we discuss the principles behind genetic studies of complex traits like JIA, and comprehensively catalog HLA candidate gene associated with JIA to date, and review several validated associations. Studies indicate that the HLA-Ⅰ, Ⅱ gene and their products play an important role in JIA pathogenesis, clinical course, hormonal effect and prognostic judgment. Studies in different ethnic groups indicate the main relationship between JIA and HLA is concentrated upon A, DR and DQ loci, especially the HLA-Ⅱ gene and some haplotypes. The different type of JIA is always with different HLA susceptible locus and protective locus. Different race, different region and different social environment also affect the JIA's susceptible gene polymorphism. Finally we discuss the problems existed in the study of JIA susceptibility and HLA polymorphism.