Populations of blue-footed boobies in the Galápagos Islands have declined by at least 50% compared with numbers recorded during the 1960s. Recently, concern has been expressed about potential adverse effects of introduced blood parasites; in particular, malarial parasites (i.e. Plasmodium sp.), which are frequently pathogenic and can cause mortality and morbidity in birds, and blood parasites of the genus Haemoproteus, which can reduce fitness. We screened blue-footed boobies at six breeding colonies within Galápagos for both genera of parasite. At two sites, we also investigated whether there was any relationship between infection status and physiological condition or breeding success. We found a high prevalence of Haemoproteus spp. in adults and chicks using PCR, although none was found on blood smears. We found no evidence of Plasmodium. Effects of parasitism on the condition of birds were limited. Also, there was no evidence that infection with Haemoproteus adversely affected breeding success or chick growth. Our results suggest that poor success of breeding birds was not strongly associated with Haemoproteus infection. However, regular colony monitoring and examination of dead birds are necessary to assess whether acute Haemoproteus infection might be responsible for some mortality, particularly of chicks.