Chemical, physical and structural analyses of polymers from explanted vascular prostheses are frequently jeopardized because of incomplete removal of the encroaching host tissue. In this study, microporous polyurethane arterial prostheses implanted as a canine thoraco-abdominal bypass were explanted after 1 and 12 months and were cleaned without fixation using four different digesting enzyme treatments, including collagenase, pancreatin and trypsin alone and collagenase and pancreatin in series, followed by washing in a solution of Triton X-100 detergent. By following this approach all the fresh tissue attached to the external and internal walls of the prostheses was removed with minimal damage to the underlying synthetic polymer. The morphology of the explanted and cleaned polyurethane prostheses could be obtained readily by light and scanning electron microscopy. Surface microporous features and the presence of polyurethane microfibres that had experienced in vivo biodegradation could therefore be identified easily. The surface and bulk physico-chemical properties of the polyurethane polymer were determined by electron spectroscopy for chemical analysis, attenuated total reflectance-Fourier transform infrared spectroscopy and differential scanning calorimetry. It was found that the most successful approach for removing fresh tissue and exposing a clean and uncontaminated polyurethane surface was to incubate the explanted samples first in collagenase followed by digestion in pancreatin. This particular cleaning technique has proved valuable in enabling us to monitor small in vivo changes in the surface chemistry and in the bulk microphase segmented structure of polyurethane biomaterials.