The liver transplant (LT) situation represents an attractive model for studying hepatocellular carcinoma (HCC) metastasis. Based on microarray data, we previously found that miR-126 expression was lower in tumor tissues of patients with post-LT HCC recurrence compared with non-recurrence. In this study, we examined the expression of miR-126 in HCC samples from 68 patients who had undergone LT using quantitative real-time PCR and analyzed its correlation with clinicopathological features and prognosis of patients. Furthermore, we performed experimental analyses to explore the involvement of miR-126 in HCC metastasis. We found that miR-126 levels were lower in tumor tissues of patients with post-LT HCC recurrence in comparison to patients with no-recurrence (p = 0.009). Lower expression of miR-126 in HCC was associated significantly with tumor recurrence (p = 0.011) and poor survival (p = 0.009) of patients. Functional studies indicated that ectopic expression of miR-126 significantly inhibits HCC cells migration, invasion, proliferation and colony formation in vitro, and suppresses experimental lung colonization in vivo. Our study revealed that down-regulation of miR-126 plays an important role in HCC metastasis, and suggest a potential application of miR-126 in prognosis prediction and HCC treatment.