Molecular classifications defining new tumor subtypes have been recently refined with genetic and transcriptomic analyses of benign and malignant hepatocellular tumors. Here, we performed microRNA (miRNA) profiling in two series of fully annotated liver tumors to uncover associations between oncogene/tumor suppressor mutations and clinical and pathological features. Expression levels of 250 miRNAs in 46 benign and malignant hepatocellular tumors were compared to those of 4 normal liver samples with quantitative reverse-transcriptase polymerase chain reaction. miRNAs associated with genetic and clinical characteristics were validated in a second series of 43 liver tumor samples and 16 nontumor samples. miRNA profiling unsupervised analysis classified samples in unique clusters characterized by histological features (tumor/nontumor,P< 0.001; benign/malignant tumors,P< 0.01; inflammatory adenoma and focal nodular hyperplasia,P< 0.01), clinical characteristics [hepatitis B virus (HBV) infection,P< 0.001; alcohol consumption,P< 0.05], and oncogene/tumor suppressor gene mutations [β-catenin,P< 0.01; hepatocyte nuclear factor 1α (HNF1α),P< 0.01]. Our study identified and validated miR-224 overexpression in all tumors and miR-200c, miR-200, miR-21, miR-224, miR-10b, and miR-222 specific deregulation in benign or malignant tumors. Moreover, miR-96 was overexpressed in HBV tumors, and miR-126* was down-regulated in alcohol-related hepatocellular carcinoma. Down-regulations of miR-107 and miR-375 were specifically associated with HNF1α and β-catenin gene mutations, respectively. miR-375 expression was highly correlated to that of β-catenin–targeted genes as miR-107 expression was correlated to that of HNF1α in a small interfering RNA cell line model. Thus, this strongly suggests that β-catenin and HNF1α could regulate miR-375 and miR-107 expression levels, respectively.Conclusion:Hepatocellular tumors may have a distinct miRNA expression fingerprint according to malignancy, risk factors, and oncogene/tumor suppressor gene alterations. Dissecting these relationships provides a new hypothesis to understand the functional impact of miRNA deregulation in liver tumorigenesis and the promising use of miRNAs as diagnostic markers.