Heparanase is an endo-β-glucuronidase that can selectively degrade heparan sulfate glycosaminoglycans and that has been shown to play a role in tumor progression, metastasis and tumor angiogenesis. Previous studies have demonstrated that the overexpression of heparanase in human tumors facilitates their invasive activity, thereby enhancing tumor metastatic potential. We detected the simultaneous and significantly correlated overexpression of heparanase in the tissues and urine of patients with bladder cancer. Expression of heparanase mRNA in the tissues was significantly correlated with various clinicopathological factors, such as stage, histological grade, size, number, recurrence and lymph node metastasis. This was not the case in the urine. In addition, the relapse rate was significantly higher in the patients exhibiting heparanase mRNA expression than in the patients lacking it. Heparanase at the mRNA level had greater sensitivity in the detection of bladder cancer than cytology, and specificity for the marker was relatively high. These findings suggest that the overexpression of heparanase may influence various malignant behaviors in bladder cancer, and that the RT-PCR assay for heparanase mRNA is a promising non-invasive test with high sensitivity and specificity for the diagnosis of the disease.