Cruzipain is a lysosomal enzyme of the flagellate Trypanosoma cruzi. It has three potential asparagine-glycosylation sites, two in the catalytic domain and one in the C-terminal domain. The latter appeared to have both high mannose- and complex-type oligosaccharides, whereas the catalytic domain only had compounds of the former type. The partial susceptibility of the complex-type compounds to endo-beta-N-acetylglucosaminidase H and their relative mannose and galactose content indicate that they had hybrid/monoantennary and biantennary structures. The same pattern of high mannose-type compounds was found at both domains, thus indicating that in cruzipain molecules having only high mannose-type compounds, all oligosaccharides were equally exposed to processing glycosidases and glycosyltransferases. As heterogenity of the protein C-terminal domain has already been detected, it is suggested that this feature might elicit an increased accessibility to processing enzymes responsible for complex-type oligosaccharide formation in certain cruzipain molecules or, alternatively, that a second glycosylation site with increased accessibility might be present in certain cruzipain molecules. Furthermore, the presence of complex-type oligosaccharides strongly suggests that, as in mammalian cells, T. cruzi lysosomal enzymes traverse the entire Golgi apparatus up to the trans-Golgi cisternae and the trans-Golgi network before reaching lysosomes.