Introduced diseases, particularly avian malaria, play a critical role in the decline and extinctions of endemic Hawaiian honeycreepers. Tolerance to avian malaria varies both within and among species. Our goal was to test whether innate immunity genes, toll-like receptors (TLRs) and β-defensins, have sufficient variation to be useful in conservation genetics research aimed at finding associations with disease tolerance. Using previously published primers, we found TLR and β-defensin genes that are variable in the three honeycreepers species studied: `amakihi (Hemignathus virens), `apapane (Himatione sanguinea) and i`iwi (Vestiaria coccinea), the last of which is highly susceptible to avian malaria. The levels of genetic diversity observed appear sufficient to justify further use in disease association studies, particularly in light of associations between avian malaria tolerance and diversity at adaptive immunity genes of the Major Histocompatibility Complex (MHC) in Hawaiian honeycreepers.