Hepatocellular carcinoma (HCC) is one of the most common malignant tumors. HCC occurs mainly in patients with chronic liver disease such as in hepatitis B and C infection. These high-risk patients are closely followed up, and increasing numbers of small equivocal lesions are detected by imaging diagnosis. They are now widely recognized as a precursor or early stage of HCC and are classified as dysplastic nodules or early HCC. It is considered that early HCC is a key step in the process of HCC development and progression. However, the molecular mechanisms of early hepatocarcinogenesis are far from clear. Specific mutations of classical oncogenes or tumor suppressor genes have not been identified in early HCC so far. Recent progress in comprehensive analysis of gene expression is shedding some light on this issue. It has been reported that HSP70, CAP2, glypican 3, and glutamine synthetase could serve as molecular markers for early HCC. Further analysis is expected to evaluate their usefulness in routine pathological diagnosis including biopsy diagnosis and also as serum markers for early detection of HCC.