Six human leucocytic antigen(HLA)-associated diseases, including ankylosing spondylitis, rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, type 1 diabetes mellitus and psoriasis, were selected as objects of this review. The characteristics of these diseases in whole-genome scans on susceptibility genes or loci undertaken to date were analyzed and compared. Meanwhile, the potential proposals for dealing with the existing problems were put forward.