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Purpose of review Primary sclerosing cholangitis (PSC) is a progressive biliary liver disorder strongly associated with inflammatory bowel disease (PSC-IBD). We summarize the genetics of PSC-IBD and highlight recent findings that further differentiate PSC-IBD as a unique disease. Recent findings To date, genome-wide studies have uncovered 23 susceptibility loci for PSC-IBD, the majority of which have been previously reported as risk factors in other immune-mediated disorders. For most candidates, the pathological relationship to PSC-IBD remains largely unknown. Several candidate genes appear to be liver related but the large majority relate to immunity and reaffirm that alterations to immune function, trafficking, and tolerance are likely to influence susceptibility and presentation of PSC-IBD. Similar to most immune-mediated diseases, the strongest association in PSC-IBD resides within the human leukocyte antigen complex and suggests that disease-specific antigens drive pathogenic immune responses. Although genetic predisposition influences disease, genetic determinants account for less than 10% of total disease liability in PSC-IBD, clearly emphasizing the predominant role of environmental factors on disease susceptibility. Summary Genetic studies define PSC-IBD as a unique disease to IBD mirroring clinical observations. Most risk loci harbour immune-related genes and disease variants are likely to perturb immune function, tolerance, and/or trafficking. Additional studies in patients and novel experimental systems are needed to identify the origin and impact of environmental factors in relation to genetic predisposition in PSC-IBD.