The etiological and pathogenic factors contributing to PBC development, progression, response to treatment, and ultimately, outcome remain a mystery. This lack of knowledge can be attributed to the complexity of PBC, wherein a number of environmental triggers may be culpable, but require coexisting genetic susceptibility to exert their effect. Recognition of the genomic regions harboring these heritable risk factors has been hindered by the rarity and late onset of PBC, which has rendered the collection of adequate numbers of patients and family members for genetic analyses a difficult task. Recent advancements in the discipline of genomics holds promise to fundamentally change our understanding, prevention, and therapy of PBC. This chance arises from the development of new high-throughput approaches to genotyping, providing the means to rapidly uncover many of the genetic polymorphisms that are relevant to disease. In order to move ahead, large registries and biospecimen repositories of patients with PBC, their family members, and well-matched controls need to be established, maintained, and continually expanded. At the same time, sizeable, comprehensive haplotype mapping based association studies of functionally plausible candidate gene groups (e.g. immune function genes) as well as more far reaching genome-wide association studies will be necessary to form the basis upon which the genetic predisposition to PBC can be defined. This first set of experimental data will provide the means for future fine mapping studies, resequencing efforts, functional experimentation, and elucidation of gene-environment and gene-gene interaction; perhaps paving new paths in PBC research.