Migratory and non-migratory passerine birds can carry several pathogens, including parasites, which may cause significant diseases in birds, other animal species and humans. Parasites have been shown to negatively impact many populations of wildlife, and this may become more significant with global temperature changes. This study was performed to investigate the prevalence of intestinal parasites in faecal samples of European passerines. Intestinal parasites identified were statistically associated with passerines phylogenetic classification, migratory habits (migratory, non-migratory) and the type of diet (omnivorous, insectivorous and granivorous). A total of 385 passerines of 42 species were captured and their droppings collected. The prevalence of parasites in faecal samples of passerines was 15.6%. Intestinal parasites were identified in 50/309 (16.2%) migratory passerines and 10/76 (13.2%) non-migratory passerines using the faecal flotation method. Coccidia were most often identified parasites; they were more likely to be present in an omnivorous bird species (p = 0.02). Syngamus spp. was more likely to be detected in omnivorous passerines (p = 0.04). Tits (p = 0.01) and finches (p = 0.006) were less likely to have intestinal parasites present in their faecal samples than passerines classified in other phylogenetic clades. Tits (p = 0.02) and finches (p = 0.008) were also less likely to have coccidia present in their faecal samples. Phylogeny was associated with the presence of parasites in faecal samples of passerines (p = 0.03). The prevalence of parasites, however, was not associated with the migration habit of passerines, but to the type of diet (p = 0.04). Our analysis suggests that the diversity of feeding sources of omnivore passerines exposes them to infection with intestinal parasites to a greater extent than granivore or insectivore passerines.