Parasites induce phenotypic modifications in their hosts, which can compromise host fitness. For example, the parasitic fly Philornis downsi, which was recently introduced to the Galapagos Islands, causes severe naris and beak malformation in Darwin's finches. The fly larvae feed on tissues from the nares of developing finch nestlings, thereby altering the size and shape of the nares and beak. Although the parasitism is age-specific (adult finches are not parasitized), naris and beak malformations persist into adulthood as parasite-induced malformations. We systematically examined adult populations of Darwin's small ground finch, Geospiza fuliginosa, on the islands of Santa Cruz for P. downsi-induced malformation. We found that malformed birds had significantly longer nares, and shorter, shallower beaks, than birds considered to be normal (i.e. with no nares or beak malformation). In addition, normal birds showed an isometry between naris length and beak dimensions (beak length feather and beak depth), which was not found in malformed birds. These differences suggest that beak morphology was influenced by P. downsi parasitism. Interestingly, we did not find any evidence of developmental impairment (smaller body size) or reduced foraging efficiency (lower body condition) between normal and malformed birds. Our findings of P. downsi-induced malformation raise new questions about the evolutionary trajectory and conservation status for this group of birds. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 577–585.