The analysis of the RUNX3 gene methylation status was conducted in the prospective group of 262 bladder cancer patients. In comparison to normal urothelium, a high frequency (63 %) of RUNX3 promoter hypermethylation was observed in tumor tissues. А statistically significant association of RUNX3 epigenetic abnormalities with a more aggressive tumor phenotype – an advanced tumor stage and grade, as well as a large tumor size – was found. We have shown that RUNX3 hypermethylation is an independent risk factor for progression and cancer-specific survival in the group of patients with non-muscle invasive bladder cancer.