Trypanosoma congolense is the agent of Nagana, the trypanosomiasis in African ruminants. Trypanosomes express an enzyme called trans-sialidase, which is believed to play an important role in maintaining pathogenicity of the parasites. Thus far, only two complete trans-sialidase sequences have been characterised, one from the American trypanosome T.cruzi and one from the African trypanosome T. brucei brucei. Although the crystal structure of T. cruzi trans-sialidase has recently been published [Buschiazzo et al., Mol. Cell 10 (2002), pp. 757 - 768], a number of questions concerning the exact transfer mechanism remain unanswered. The availability of further trans-sialidase sequences will ensure a better understanding of how transfer activity can be achieved and will provide the opportunity to develop highly specific, structure-based trans-sialidase inhibitors. Utilising a PCR-based approach two different trans-sialidase gene copies from T. congolense were identified, which share only 50% identity with each other, but show significant similarity with known viral, bacterial and trypanosomal sialidases and trans-sialidases. In both partial sequences most of the critical active siteresidues common to other trypanosomal sialidases and trans-sialidases are conserved. This is further illustrated by modelling the active site of the longer of the two partial gene sequences.