This editorial introduces a research topic collection of 10 articles examining HLA and non-HLA gene associations with autoimmune liver diseases (primary biliary cholangitis and autoimmune hepatitis) across diverse populations. The collection reports HLA predisposition alleles, a protective metabolite (inosine) in a murine model, epigenetic influences, and microbiome roles, while noting that neither HLA genes nor non-HLA genes alone fully explain disease development.