This study compares the sensitivity of two methods for diagnosing avian haemosporidian parasite (Plasmodium, Haemoproteus and Leucocytozoon) prevalence in Siberian tits Poecile cinctus breeding in northern Finland: a polymerase chain reaction (PCR)-based method and microscopy examination of blood smears. During molecular analysis, we used PCR screening and RFLP as a post-PCR diagnostic step. PCR screening detected haemosporidian parasites in the blood of 38 out of 40 (95%) breeding Siberian tits. Microscopy examination of blood smears and PCR diagnostics showed the same prevalences for Leucocytozoon spp. infections. In contrast, prevalences of Haemoproteus spp. and Plasmodium spp. determined by molecular methods were significantly higher than the prevalence determined by microscopy screening. However, habitat and sex effects on the total count of parasites, Plasmodium spp., Haemoproteus spp. and Leucocytozoon spp. counts appeared to be similar when assessed with either screening method, giving the same interpretation for the ecological hypotheses tested. Finally, this study shows that transmission of avian malaria can occur in the area of the Arctic Circle in northern Europe.