Primary biliary cholangitis (PBC) is a rare autoimmune disease with a clear predisposition for human leukocyte antigen(HLA)-DR/DQ-associated loss of immune tolerance for the E2 component of the pyruvate dehydrogenase complex. Three-field-resolutionHLAimputation of 1,670 Japanese PBC patients and 2,328 healthy controls was conducted using Japanese population-specificHLAreference panels. Eighteen previously reported Japanese PBC-associatedHLAalleles were confirmed and extended to 3-field-resolution, includingHLA-DRB1*08:03toHLA-DRB1*08:03:02,HLA-DQB1*03:01toHLA-DQB1*03:01:01,HLA-DQB1*04:01toHLA-DQB1*04:01:01andHLA-DQB1*06:04toHLA-DQB1*06:04:01. In addition, additional significant novelHLAalleles were identified, including 3 novel susceptibleHLA-DQA1alleles:HLA-DQA1*03:03:01,HLA-DQA1*04:01:01,HLA-DQA1*01:04:01and 1 novel protectiveHLA-DQA1allele,HLA-DQA1*05:05:01. In addition, PBC patients carryingHLA-DRB1*15:01:01andHLA-DQA1*03:03:01would have a higher predisposition toward developing concomitant autoimmune hepatitis (AIH). Further, late-stage and symptomatic PBC shared the same susceptibleHLAalleles ofHLA-A*26:01:01,HLA-DRB1*09:01:02andHLA-DQB1*03:03:02. Lastly,HLA-DPB1*05:01:01was identified as a potential riskHLAallele for development of hepatocellular carcinoma (HCC) in PBC patients. In conclusion, we have extended the current knowledge ofHLAallele associations to 3-field resolution and identified novelHLAallele associations with predisposition risk, staging, symptomatic state, and AIH and HCC events for Japanese PBC patients.