The ability of tumour cells to metastasize and the vascularization of solid tumours by angiogenesis is linked to the enzymatic properties of the endo-β-glucuronidase Heparanase.  Consequently there is substantial interest in inhibiting Heparanase activity using small molecule antagonists for treating the growth and spread of cancer.  The determination of the structure of Heparanase would greatly aid the development of drugs targeting its activity.  Due to significant posttranslational modifications of Heparanase in mammalian systems, particularly the crucial heterodimer formation for biological activity, it has proven challenging to produce sufficient quantities of active heparanase in prokaryotic expression systems suitable for structural studies.  Recently a second stand-alone Heparanase domain was identified at the C-terminus, which mediates the non-enzymatic functions of Heparanase.  Importantly, this C-terminal domain has lower levels of post-translational modification, making it a potential candidate for expression on its own in prokaryotic expression systems.  This study demonstrates that even with engineered prokaryotic cell strains that mimic post-translation mammalian machineries, no in vivo biologically active protein was expressed.  However in vitro refolding from inclusion bodies recovered after protein expression yielded folded protein in quantities suitable for structural analysis by Circular Dichroism (CD) Spectroscopy.  CD spectroscopy revealed a primarily β-strand topology, which is in agreement with predictions based on a homology model of the C-terminal domain of Heparanase.  Although folded material was obtained, the protein exhibited instability at high concentrations, thus hampering attempts at crystallographic analysis.  Further optimization will be required to enable the production of recombinant protein in prokaryotic systems that may enable crystallographic studies to guide drug design strategies for the development of Heparanase-based cancer therapies.