We investigated the presence of both Neospora caninum and Toxoplasma gondii in 250 brain tissue samples from 9 species of feral rodents and insectivores caught on 10 organic farms in the Netherlands in 2004. Collected samples were conserved in 4% paraformaldehyde solution and analysed by real-time PCR. For N. caninum, 31 samples originating from 6 species tested positive (12.4%): common shrews (33.3%), wood mice (17.6%), harvest mice (16.7%), house mice (15.4%), white-toothed shrews (10.8%) and common voles (4.2%). For T. gondii, the overall contamination level was 4%, and only three species were found to be positive: house mice (9.0%), common voles (4.2%) and white-toothed shrews (2.0%). Most N. caninum infected samples (27/31; 87%) were found on farms where dogs were present. Due to the observation that rodents and insectivores can contract both parasites, they might function as indicator species for the parasitic load on farms.