Avian malaria parasites can negatively affect many aspects of the life of the passerines. Though these parasites may strongly affect the health and thus migration patterns of the birds also during autumn, previous studies on avian malaria focused mainly on the spring migration and the breeding periods of the birds. We investigated whether the prevalence of blood parasites varies in relation to biometrical traits, body condition and arrival time in the European Robin (Erithacus rubecula) during autumn migration. We found no sex or age related differences in avian malaria prevalence and no relationship between infection status and body size or actual condition of the birds was found either. However, the timing of autumn migration differed marginally between infected and non-infected juveniles, so that parasitized individuals arrived later at the Hungarian stopover site. This is either because avian malaria infections adversely affect the migration timing or migration speed of the birds, or because later arriving individuals come from more distant populations with possibly higher blood parasite prevalence. The possible delay that parasites cause in the arrival time of the birds during autumn migration could affect the whole migratory strategy and the breeding success of the birds in the next season.