Purpose To determine the association between mutations in CDKN2A and FGFR3 genes and the diagnosis of bladder carcinoma (BCa). Methods A systematic search strategy was carried out through MEDLINE, EMBASE, LILACS, CENTRAL and unpublished literature. We included RCTs, cohort, case-control and cross-sectional studies that involved patients > 18-year-old assessing the association between CDKN2A and FGFR3 mutated genes and BCa. The primary outcome was bladder cancer defined by histology of the sample. We assessed the risk of bias with QUADAS2 and performed a meta-analysis with Review Manager v5.3. Results We found 97 records with the search strategies. After duplicates were removed, six studies were included in metaanalysis. Regarding the association between mutated FGFR3 and bladder cancer, we found an OR 31 95% CI (15-64). However, there was no association for CDKN2A and BCa. Conclusion There is a strong association between FGFR3 mutated gene and the diagnosis of bladder cancer, which has not been observed with CDKN2A. Such a result supports FGFR3 mutated gene as a promissory bladder cancer screening and monitoring biomarker.