Human leukocyte antigen (HLA) class II beta chain plays an important role in the recognition of foreign antigens in immune reactions. Different forms of immune reaction may be concerned with initiation and progression of infectious diseases such as periodontitis. In this study we examined the frequency of HLA class II serotype and the variation of HLA class II beta gene in periodontitis patients. HLA serotypic frequencies in 70 Japanese patients with periodontitis and 26 individuals with periodontal health were examined. No HLA serotype specific to any type of periodontitis was observed. In order to detect differences among some HLA serotypes, restriction fragment length polymorphism (RFLP) analysis was undertaken with cDNA probes for HLA-DR beta and HLA-DQ beta genes in 20 subjects (15 patients and 5 healthy individuals). Atypical BamHI and EcoRI restriction sites were found in the HLA-DQ beta gene from 3 patients with early-onset periodontitis. In addition to these 20 subjects, an additional 80 subjects (40 patients and 40 healthy individuals) were screened for the atypical BamHI restriction site using the polymerase chain reaction method. It was detected in 7 patients with early-onset periodontitis, 1 patient with adult periodontitis, and 3 healthy subjects. No clinical differences except age were found between patients with this gene variation and other patients. Interestingly, all 3 healthy subjects with this gene variation were from subjects whose family members developed early-onset periodontitis with the gene variation. Atypical BamHI and EcoRI restriction sites and 41-nt repeated sequence were found in the intron before the third exon of HLA-DQB gene. These results suggest that these intronic gene variations may be useful as gene markers for a subpopulation of early-onset periodontitis and might affect immune reactions such as antigen recognition.