The aim of this study is to examine the possible application of Random amplified polymorphic DNA (RAPD) technique based on the polymerase chain reaction (PCR) method, as a genetic test for identifying the significant genomic alterations in bladder cancer patients. DNAs were extracted from the exfoliated cells in the urine of 50 male bladder cancer patients, using the Phenol-Chloroform DNA extraction method, and the yielded DNAs were amplified with the BioA-09 random primer (5`-GGGTAACGCC-3`). The amplified PCR products from RAPD analysis were electrophoretically separated in agarose gels; banding profiles were visualized by ethidium bromide staining and demonstrated under ultraviolet light. The genomic alterations were clearly apparent in tumor RAPD-PCR patterns, by the loss of normal bands and the appearance of new tumor-related bands, as compared to the controls. The correlation between the genomic alteration and the histopathological subtypes was assessed using the X² test. In addition, bands with molecular sizes 500 (p < 0.001) and 1300 (p = 0.033) bp were used as molecular markers for transitional cell carcinoma, while squamous cell carcinoma type had two diagnostic bands with molecular sizes 1800 (p < 0.001) and 1400 (p < 0.021) bps, respectively. Our study suggests the potential of RAPD-PCR method to produce diagnostic markers for analysing the genomic instabilities in bladder tumors.