More than 13 thousand cases of bladder cancer are registered in Russia annually that represents an actual problem in modern urologic oncology. Searching and characterization of new molecular markers of non-muscle invasive bladder cancer (NMIBC – 80% of bladder cancer cases), identified in tumor cells from urine sediment are needed. We have provided complex analysis of mutations in the key oncogenes of NMIBC using PCR and subsequent sequencing of exons 7 and 10 of the gene FGFR3, exons 9 and 20 of the gene PIK3CA. NMIBC cohort includes 22 samples of DNA from urine sediments; control group consists 24 patients with cystitis and urolithiasis. Missense-mutations was detected in 32% NMIBC samples but not in controls. According databases ClinVar, COSMIC and HGMD most of them have been identified as pathogenic DNA-changes during carcinogenesis. Perhaps the panel with aforementioned genes and TERT promoter as addition locus with using allele-specific PCR or other method for the preferential amplification of mutant alleles could form the basis for the development a system of markers in non-invasive molecular genetic diagnostics of NMIBC.