Blood feeding insects are vectors of a wide range of pathogens that cause diseases of human and veterinary importance, including leishmaniasis transmitted by phlebotomine sand flies. During blood feeding, hematophagus insects inject saliva into the skin of the host. Vector saliva contains molecules that interfere with the host’s coagulation cascade, induce vasodilation and cause inflammation. Sand fly saliva exacerbates Leishmania infection in animal models; however, repeated exposure of animals to either bites or salivary gland homogenates of Phlebotomus papatasi protects against L. major. Additionally, animals vaccinated with one salivary gland antigen, SP15, develop a delayed type hypersensitivity (DTH)-associated protection against challenge with Leishmania. We are investigating amino acid sequence variability for secreted salivary gland proteins from field populations of P. papatasi from Egypt and Jordan. Salivary gland cDNAs from secreted proteins were PCR amplified, sequenced and results compiled using various bioinformatics tools. For each protein, predicted MHC class II T-cell epitopes were obtained and compared to areas of amino acid sequence variability. Five salivary gland proteins (SP15, SP29-Antigen5, SP32, SP42 and SP44) were compared. Our results indicate that SP15 has at least 3 additional haplotypes more than was previously suggested and that at least nine MCH class II T-cell epitopes are predicted in regions of variability of the protein. Furthermore, the data indicate that SP29 (Antigen5) has the lowest and SP42 has the highest haplotype number of the proteins analyzed. Mapping the amino acid variability and MHC class II prediction epitope sites in sand fly salivary gland proteins is a crucial step in defining saliva-based vaccine candidates.