Background: Cluster of differentiation 44 (CD44) is an important surface marker of cancer stem cells in a variety of tumors. A number of previous studies have been conducted to investigate the association between CD44 gene rs13347 C>T polymorphism and cancer risk in humans; nevertheless, the results remain controversial. We therefore performed this meta-analysis to confirm the role of this polymorphism in susceptibility to human cancer. Materials and methods: The studies published up to December 2015 were searched in PubMed, Web of Science, and China National Knowledge Infrastructure databases. Twelve eligible case-control studies were identified, involving a total of 6,982 cases and 7,430 controls. Pooled odds ratio (OR) and corresponding 95% confidence interval (CI) were calculated using a fixed or random-effect model to estimate the strength of the association. Results: The results of the overall analyses indicated that CD44 gene rs13347 polymorphism was significantly associated with cancer risk in Asians (CT vs CC: OR = 1.35, 95% CI = 1.12-1.62; TT vs CC: OR = 1.99, 95% CI = 1.52-2.60; TT + CT vs CC: OR = 1.41, 95% CI = 1.16-1.71; and TT vs CC + CT: OR = 1.74, 95% CI = 1.41-2.14), especially in Chinese population (CT vs CC: OR = 1.42, 95% CI = 1.16-1.75; TT vs CC: OR = 2.13, 95% CI = 1.58-2.86; TT + CT vs CC: OR = 1.50, 95% CI = 1.21-1.87; and TT vs CC + CT: OR = 1.80, 95% CI = 1.43-2.26). In stratified analyses by cancer types, there was evidence for an association between this polymorphism and nasopharyngeal cancer and breast cancer, respectively. Conclusion: The results of this meta-analysis suggest that the CD44 gene rs13347 C>T polymorphism is associated with elevated risk of human cancer in Asians, especially in Chinese population. Further well-designed studies on a larger population covering other ethnicities should be carried out to validate our results.