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Bladder cancer is a heterogenous malignancy with wide scale of clinical manifestation. Different chromosomal aberrations have been already identified in bladder tumors. These aberrations can be detected by multicolor interphase fluorescence in situ hybridization (I-FISH) or comparative genomic hybridization (CGH). The aim of this study was to determine the diagnostic benefits of non-invasive I-FISH method and to comprehensively characterise genetic alterations using CGH in selected patients with bladder tumors. We examined 128 urine samples and correlated our results with histological findings. I-FISH using UroVysion kit showed positivity in 63,6 % of G1 tumors, 64,3 % of G2 tumors and 91,7 % in G3 tumors. We examined also 12 bladder tissue samples by means of CGH and various genetic alterations were ascertained independent on tumor grade. The most frequent gains and losses of DNA material were detected on chromosomes 1, 8, 9, 10, 11, 13, and 14. The contribution of I-FISH is in an early and non-invasive detection of bladder cancer recurrences during follow up of patients after the surgery. CGH provides information about further genetic alterations and some of them could be ascertained as recurrent changes with prognostic significance.