Background: Periodontitis is a pathological inflammatory condition of the periodontal tissues surrounding the teeth. It is a multiple factor disease caused by genetic factors, environmental factors, and periodontal bacteria. Human leukocyte antigen is the most polymorphic genetic system in man. Genes of this region influence susceptibility to certain diseases including periodontitis. Objectives: This study was established to shed light on the possible association of HLA class II (HLA-DQB1) alleles with chronic periodontitis. Materials and Methods: The study involved 40 Iraqi patients with chronic periodontitis and 40 healthy controls. Periodontal parameters used in this study were plaque index (PI), gingival index (GI), probing pocket depth (PPD) and clinical attachment level. DNA was extracted from a blood sample taken from each subject, then HLA-DQB1 gene was amplified using sequence specific oligonucleotide primed PCR (PCR-SSO). Genotyping of HLA-DQB1 alleles were performed using a reverse a hybridization automatic line probe assay (Auto-LiPA). Results: There was an increased frequency of HLA-DQB1*05:02 allele in patients as compared to controls group (25% and 7.5% respectively) with P=0.04 and odds ratio=4.11. In contrast, the frequency of DQB1*03:01 allele was higher among controls group as compared to periodontitis patients ((P=0.04, odds ratio=4·11). Conclusion: Our data show a correlation between the HLA-DQB1 locus and the occurrence of periodontitis in Iraq, supporting DQB1*05:02 as a predisposing allele for this disease.