Background and aimsHepatic immune cell analysis is critical for understanding chronic inflammatory liver diseases, such as primary sclerosing cholangitis (PSC) and steatotic liver disease. However, liver immunoprofiling is limited due to reliance on end-stage disease liver explants. Fine needle aspiration (FNA) is a minimally invasive technique that can overcome these limitations. We evaluate the safety and efficacy of liver FNA to profile hepatic immune subsets in non-infectious liver conditions.MethodsFlow cytometry and single-cell RNA sequencing (scRNA-seq) were used to compare the hepatic immune cell composition and gene expression to that of matched peripheral blood mononuclear cells (PBMCs).ResultsWe obtained liver FNAs from 38 patients. The median pain score was 0. No serious adverse effects were reported. Flow cytometry demonstrated enrichment of CD69+ T and natural killer (NK) cells in the liver (all Padj < 0.05). ScRNA-seq of 38 012 hepatic immune cells and 78 751 PBMCs in a patient subset showed specific enrichment of CXCR6+ NK, CD8+ central memory T, and mucosal-associated invariant T (MAIT) cells in the liver, and relatively lower CD4+ regulatory T cell (Treg) abundance (all Padj < 0.05). Gene expression and cell-cell interaction analyses revealed increases in cytokine production, signalling, and responsiveness in hepatic immune cells compared to PBMCs.ConclusionsFNA sampling is a safe approach for investigating the inflammatory landscape of PSC and other liver diseases. Single-cell profiling reveals that FNAs capture tissue-specific immune cell types and gene expression differences, suggesting this sampling method may provide a basis for future experimental medicine analyses.