Background: CD44 has been reported to be involved with tumor growth and metastasis and has also been implicated as a CSC marker in hepatocellular carcinoma (HCC). However, the prognostic value of CD44 still remains controversial; hence, we investigated the correlation between CD44 and the clinicopathological features of HCC by meta-analysis. Methods: Identification and review of publications assessing clinical or prognostic significance of CD44 expression in HCC until November 1, 2015. A meta-analysis was performed to clarify the association between CD44 expression and clinical outcomes. Results: A total of 14 publications met the criteria and comprised 2235 cases. Analysis of these data showed that CD44 expression was not significantly associated with the tumor differentiation (OR 1.48, 95 % confidence interval [CI] 0.85-2.60, P = 0.17), AFP level of HCC patients (OR 0.83, 95 % CI 0.52-1.33, P = 0.45), or disease-free survival (relative risk [RR] 1.15, 95 % CI, 0.85-1.54; P = 0.36). However, in the identified studies, CD44 expression was highly correlated with tumor TNM classification (OR 2.38, 95 % CI 1.23-4.60; P = 0.01) and decreased overall survival (RR 1.49, 95 % CI, 1.26-1.76; P < 0.00001). Conclusions: This meta-analysis shows CD44 expression in HCC is connected with decreased overall and thus marks a worse prognosis.