Cardiomyopathies (CMs) are primary disorders of cardiac muscle. They are a major cause of morbidity and mortality for all ages and, like acquired forms of cardiovascular disease, often result in heart failure. Molecular genetic studies have made remarkable progress in defining the pathogenesis of CM. The present study was the first report to evaluate the relationship between class II major histocompatibility complex (MHC) genes (HLA-DRB1 and HLA-DQB1) and the genetic susceptibility to primary dilated cardiomyopathy (DCM) in Tunisian patients. The human leukocyte antigen (HLA)-DRB1 and -DQB1 alleles were analyzed in 76 patients with primary DCM and 111 ethnically matched healthy controls using polymerase chain reaction-sequence specific primers technique. An increased frequencies of HLA-DRB1*0401 (OR = 2.67, P < 0.001), HLA-DQB1*0302 (OR = 3.28, P = 0.001) and HLA-DQB1*0401 (OR = 6.26, P = 0.005) alleles were found in the patients with primary DCM compared with healthy controls. Individuals with HLA-DRB1*1301 (OR = 0.24, P < 0.001) and HLA-DQB1*0201 (OR = 0.49, P = 0.002) alleles have a protective effect against primary DCM. Two haplotypes were associated with increased risk of primary DCM: DRB1*0401/DQB1*0302 (OR = 4.53, P = 0.002) and DRB1*0401/DQB1*0401 (OR = 9.42, P = 0.004). In conclusion, our data suggest that the variation in class II HLA alleles could be a genetic factor involved in the susceptibility to primary DCM in the Tunisian population.