Cancer stem cells (CSCs) are responsible for cancer recurrence and metastasis and are related to poor prognosis in patients with hepatocellular carcinoma (HCC). CD133 is one of the most commonly used CSC markers. In this study, expression and the biological significance of CSC marker CD133 was evaluated in HCC, at mRNA and protein levels. We demonstrate that both mRNA and protein levels of CD133 are significantly elevated in HCC relative to that in adjacent non-cancerous tissue based on bioinformatics and immunohistochemical analysis, respectively (P < 0.01). Intriguingly, we detected nuclear distribution of CD133 and found that nuclear CD133 expression was indicative of poor patient prognosis (median survival 12 months versus 34.5 months) (Log-Rank, P = 0.0258). Meanwhile, our findings suggest that nuclear CD133 expression is positively correlated with tumor size and serves as an independent prognostic factor for HCC after surgical resection (HR = 0.564, 95% CI 0.313-1.018, P = 0.057). Nuclear CD133 expression can potentially serve as a biomarker for clinical diagnosis and prognosis of HCC. IJCEP Copyright © 2018.