A sixth locus (vsp417-6) belonging to the vsp417 gene subfamily, a subset of the family of genes that encodes 'variant-specific' surface proteins (VSP) in Giardia, is described. The sequence of vsp417-6(A-I), the ortholog representing the vsp417-6 locus in isolates of the type A-I (Assemblage A, Group I) genotype of Giardia intestinalis, was determined from a cloned 5.5-kb Hind III fragment of genomic DNA derived from isolate Ad-1/C1. The gene encodes a 704 residue polypeptide (VSP417-6(A-I), Mr 71,674) that has 75% identity (92% similarity) over a 718 residue overlap with the prototype of the VSP417 subfamily, VSP417-1(A-I)-encoded by the vsp417-1 (syn. tsa417) locus in type A-I isolates. Alignment of VSP417-6(A-I) with the deduced sequences of other known members of this subfamily identified one polypeptide, encoded by a gene found in type A-II (Assemblage A, Group II) isolates, whose homology with VSP417-6(A-I) (91% identity, 98% similarity over 713-residues) indicated that it was VSP417-6(A-II), the VSP417-6 ortholog in type A-II isolates. Sequence-based phylogenetic analyses of known VSP417 subfamily members defined several loci that predate the emergence of the A-I and A-II sublineages of G. intestinalis. Related sequences that may correspond to additional, uncharacterised vsp417 subfamily genes were identified in genomic DNA by Southern hybridisation using subfamily- and locus-specific probes. Variant-specific expression of vsp417-1 and vsp417-6 within axenic cultures of G. intestinalis was detected by in situ mRNA hybridization, indicating that these genes are functional and that they are expressed in an alternative fashion with other vsp genes in these organisms.