Protein phosphatase of regenerating liver 3 (PRL-3) is a metastasis-associated phosphatase. Studies have shown that its overexpression increases cell motility and invasiveness. In this study, we aimed to investigate the expression of PRL-3 in hepatocellular carcinoma (HCC) tumor tissues and determine its correlations with matrix metalloproteinases (MMP-2, MMP-9) and E-cadherin in HCC. Paired cancerous and non-cancerous tissues were freshly collected from 42 primary HCC patients. PRL-3 expression at both mRNA and protein level was evaluated by real-time PCR, Western blot analysis and immunohistochemistry. The microvessel density (MVD) in HCC was detected with immunohistochemistry. The mRNA expression of MMP-2, MMP-9 and E-cadherin was analyzed by real-time PCR in search of correlations with PRL-3. We found that PRL-3 was significantly up-regulated in the HCC tumor tissues compared with corresponding noncancerous liver tissues (0.664+/-0.053 vs. 0.024+/-0.003, P<0.001). The mRNA level of PRL-3 in tissues was correlated with serum alpha-fetoprotein level, vascular invasion and metastasis (P<0.001). PRL-3 expression was closely related to MVD. Furthermore, we found a significant correlation between PRL-3 mRNA expression and MMP-2, MMP-9 and E-cadherin. Our results demonstrated that PRL-3 is up-regulated in HCC. It is strongly suggested that PRL-3 plays a key role in the angiogenesis and invasion of HCC. MMP-2, MMP-9 and E-cadherin might be involved in PRL-3 functions in HCC.