Hepatocellular adenomas (HCA) are rare, benign liver tumours that often occur in women of reproductive age. HCA has been associated with the use of oral contraceptives, but the increased incidence of the tumour in older women and in men has linked the tumour type to other diseases, including the metabolic syndrome. Genotypical classification of the adenomas has led to the identification of four subgroups that correlate genotype with phenotype: human hepatocyte nuclear factor-1 alpha (HNF1α) inactivating HCA, β-catenin activating HCA, inflammatory HCA and unclassified HCA. HNF1α inactivating HCA is associated with bi-allelic mutations in the TCF1 gene and morphologically has marked steatosis. β-catenin activating HCA has increased activity of the Wnt/β-catenin pathway and is associated with possible malignant transformation. Inflammatory HCA is characterized by an oncogene-induced inflammation due to alterations in the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway. In the diagnostic setting, sub classification of HCA is based primarily on immunohistochemical analyzes, and has had an increasing impact on choice of treatment and individual prognostic assessment. This review offers an overview of the reported gene mutations associated with hepatocellular adenomas together with a discussion of the diagnostic and prognostic value.