The obligate dipterian bird parasite Philornis downsi and the facultative parasitic fly Sarcodexia lambens were, until recently, unknown on the Galápagos archipelago. The first sign of parasitism of P. downsi on Darwin's finches was found in 1997. Parasitism data were collected from 177 nests of 12 bird species, including eight endemic species. In this study we examined host specificity, infection prevalence (percentage of infested nests), parasite load per nest and per nestling, and breeding success for two climatically different years, 1998 and 2000. We found Philornis downsi in 97% of the investigated nests, Sarcodexia lambens in 32% of the nests and a still unidentified endoparasitic Muscidae in 87% of the clutches investigated. The first two ectoparasites showed no host preference and were found in the dry deciduous coastal zone as well as in the evergreen moist forest. Parasite load per nest varied through the breeding stages, with no parasites during incubation, but with numbers increasing with nestling development. Parasite load per nest showed little variation, but variation in brood size led to different infestation rates per nestling. Small broods suffered higher parasite loads and higher nestling mortality, thus inducing a possible impact on population dynamics.