A gene (vsp417-3A-II) encoding a new member of the variant-specific surface protein (VSP) family of Giardia is described. Vsp417-3A-II is detected exclusively in isolates belonging to the genetic Assemblage A/Group II sublineage of G. intestinalis, and it is closely related to a previously characterized VSP gene (tsp11, herein renamed vsp417-2A-I) found in Group I isolates of G. intestinalis. Analysis of DNA amplified from the genomes of Group II isolates using consensus primers also revealed products corresponding to the vsp417-2 locus (vsp417-2A-II allele), indicating that vsp417-2A-II and vsp417-3A-II represent separate loci in these organisms. Southern hybridizations revealed a single genomic copy of vsp417-3A-II in Group II isolates, but efforts to detect this locus in Group I organisms were unsuccessful. Together with the vsp417-1 (tsa417) locus that was first identified in the genetic Group I isolate WB and which has been detected since in all tested genetic Group I isolates (as vsp417-1A-I) and in genetic Group II isolates (as vsp417-1A-II), vsp417-3A-II represents a third member of a stable subset of tsa417-like VSP genes in genetic Group II G. intestinalis. The encoded polypeptide, vsp417-3A-II (667 residues, predicted Mr 69120) possesses a high cysteine content (12·1 mol%), 28 copies of the metal-binding -CXXC- motif, and a highly conserved C-terminal hydrophobic domain – similar to all other characterized Giardia VSP. A revised nomenclature for Giardia VSP genes is proposed, prompted by the need to describe the homologues found in the various major genotypes of the species complex, G. intestinalis.