Epithelial cell adhesion molecule (EpCAM) has been proposed as a marker for cancer stem cells in human hepatocellular carcinoma (HCC). However, the function and clinical significance of EpCAM in HCC is largely unknown. We examined EpCAM expression and localization in 28 dysplastic nodules (DNs) and their corresponding cirrhotic nodules, 79 HCC tissue sections and 132 HCC tissue microarray cores by immunohistochemistry and determined the relationship to clinicopathologic findings. We also examined the role of EpCAM in HCC using synthetic small interfering RNA to silence EpCAM gene expression in Huh-7 cells. EpCAM expression was very rare in DNs but dominantly appeared in a distinctly nodular type of small HCC. Expression of EpCAM was observed in 39% (31/79) of HCC tissue sections and in 34.1% (45/132) of tissue microarray sections. EpCAM expression in HCC was significantly associated with high tumor grade and serum α-fetoprotein level. Silencing EpCAM gene expression significantly decreased the proliferative activity and invasiveness of HCC cells. EpCAM expression was an independent prognostic factor for survival in patients with T1 HCC. The data indicate that EpCAM expression occurs at distinct nodular stage of HCC and could play an important role in HCC progression.