A simple and rapid capillary zone electrophoresis method has been developed and validated for determination of heparin in a pharmaceutical product and evaluation of heparin stability under different stress conditions. The best separation was achieved by a bare fused silica capillary (50 μm i.d.; 50 cm total and 41.5 cm effective length), phosphate buffer (pH=3.50, 72 mM) at 35°C, hydrodynamic injection at 50 mbar for 40 seconds and applied voltage of-30 kV. Heparin and force degradation products were detected by a photo diode array detector at 200 nm and 257 nm, respectively. The proposed method was validated in terms of linearity, accuracy, precision, limit of quantification (LOQ) and limit of detection (LOD). For evaluation of heparin stability, heparin solutions were subjected to thermal (90 ± 1°C), acidic (pH=2.00, 70 ± 1°C) and basic (pH=12.00, 70 ± 1°C) stress conditions, also sun light exposure (in the lab). The results indicated that, the method was linear in the range of 0.312 to 15.0 mg/ml with LOD of 0.078 mg/ ml and LOQ of 0.312 mg/ml, accurate (between 97.27% and 101.0%) and precise (intra-day precision of 0.28 to 1.8 and inter-day precision of 0.78 to 3.2%). The migration time of heparin under optimized conditions, was 2.39 ± 0.03 minutes and force degradation products were separated within 7 minutes. Heparin content in the pharmaceutical product quantified by the method was 99.58 ± 0.70% of the label claim. Meanwhile the method could show the changes in the heparin electropherogram, also formation of degradation products under different stress conditions. Therefore the proposed method could be applied as a fast and suitable technique for determination of heparin in pharmaceutical dosage forms and stability studies.