Crystals of dengue serotype 2 and West Nile virus NS2B-NS3 protease complexes have been obtained and the crystals of both diffract to useful resolution. Sample homogeneity was essential for obtaining X-ray-quality crystals of the dengue protease. Controlled proteolysis produced a crystallizable fragment of the apo West Nile virus NS2B-NS3 and crystals were also obtained in the presence of a peptidic inhibitor.