Capillary zone electrophoresis (CZE) was used to investigate interactions between heparin and programmed cell death 5 (PDCD5), and between heparin and PDCD5-related peptides. Samples containing PDCD5, PDCD5-related peptides, and heparin at various ratios were incubated at room temperature and then separated by CZE with tris-acetate buffer at pH 7.2. Both qualitative and quantitative characterizations of the binding of PDCD5 and PDCD5-related peptides to heparin were determined. The changes in the signals of PDCD5 and PDCD5-related peptides were monitored by comparing the electropherograms of the mixtures containing PDCD5 and heparin and PDCD5-related peptides and heparin with that of PDCD5 or PDCD5-related peptides only. The binding constant of the interaction between PDCD5 and heparin was calculated as 4.17∈×∈10M by Scatchard analysis. Our investigations show that it is possible to characterize the interaction between PDCD5 and heparin quantitatively and the interaction between PDCD5-related peptides and heparin qualitatively using CZE. © Springer-Verlag 2007.