Autoimmune liver diseases are sometimes difficult to differentiate from hepatic overlap syndromes (OS). The objective of this study was to use polymorphic genetic markers to better distinguish clinical heterogeneity in autoimmune liver disease. Since autoimmunity is the result of autoantibody production we studied HLA-DR alleles in 20 patients with autoimmune hepatitis (AIH), 16 with primary biliary cirrhosis (PBC), 10 with OS, and in 99 ethnically matched healthy individuals. Patients with OS had significantly higher alkaline phosphatase and total bilirubin levels than patients with AIH. OS patients had a higher prevalence of positive antinuclear antibodies and a higher AIH score than patients with PBC. Patients with OS also had higher total immunoglobulin levels (IgG isotype) as compared to patients with PBC. We found in PBC patients a higher gene frequency of HLA-DR4 and DR1 as compared to healthy controls (p = 0.03, OR = 2.2 and p = 0.004, OR = 4.3, respectively) and to OS patients (p = 0.01, OR = 6.8, and p = 0.004, OR = 10.0, respectively). On the other hand, the gene frequency of HLADR5 was significantly decreased in the total group of patients as compared to healthy controls suggesting a protective role of this allele for developing autoimmune liver disease.