To establish a capillary electrophoresis (CE) method to determine the value of urinary heparin in bladder transitional cell carcinoma (BTCC). Methods Reverse polarity CE with a UV-detector 190 nm in a 20kV and pH2. 5 buffer system was used to determine urinary heparin in 21 patients with BTCC and 12 normal individuals. The analysis of variance (ANOVA) was used in this experiment and significance level is 0. 0.5. Results The correlation with heparin peak area and its value is linear. The value of urinary haparin is (0.94± 0. 48) μ/L in 12 normal, (1. 30±0.73) μg/L in 11 patients with Ta～T1 BTCC and (0. 54±0. 45) ug/L in 10 patients with T2～T1 BTCC. Urinary heparin was lower in T2～T1 BTCC than in normal and Ta～T1 BTCC (P<0. 05). Conclusion Reverse polarity CE is a high-resolution, rapid and simple method to separate heparin from urine. Falling of urinary heparin in BTCC plays an important role in the infiltration and transition of the carcinoma cells.