Background: The correlation between G388R, V10I polymorphisms of fibroblast growth factor receptor (FGFR) 4 gene and risk of carcinoma has been investigated previously, but the results are contradictory.Methods: Odds ratios (ORs) with 95% confidence intervals (95% CIs), in silico tools and immunohistochemical staining (IHS) were adopted to assess the association. Results: Totally, 13,793 cancer patients and 16,179 controls were evaluated in the pooled analysis. When all the studies were summarized, we found that G388R polymorphism is associated with elevated susceptibility to cancer under homozygous comparison (OR = 1.21, 95%CI = 1.03 - 1.43, P = 0.020) and recessive genetic model (OR = 1.21, 95%CI = 1.04 - 1.41, P = 0.012). In stratification analysis by cancer type and ethnicity, similar findings were indicated in prostate cancer, breast cancer, and Asian descendants. Polyphen2 bioinformatics analysis showed that the G388R mutation is predicted to be possibly damaging to the protein function of FGFR4. IHS analysis indicated that the FGFR4 expression is increased in more advanced prostate cancer. Conclusion: FGFR4 G388R polymorphism may be associated with cancer risk, especially in prostate cancer, breast cancer, and Asian descendants. Up-regulation of FGFR4 may be related to a poor prognosis in prostate cancer.