The aim of the study was to determine the prevalence and intensity of parasite infection of the digestive tract in sheep and goats from the West Pomerania region following anti-parasite treatment. Feces were freely collected from sheep and goats kept on organic farms and subjected to analysis by the Willis-Schlaf and McMaster’s flotation methods. The mean extensity of infection by gastrointestinal parasites in both sheep and goats was found to be 100%. Both sheep and goats displayed the presence of gastrointestinal nematodes, Eimeria protozoa and Moniezia spp. tapeworms. The intensity of infection of sheep and goats by these parasites was arranged as follows: gastrointestinal nematodes > Eimeria protozoa > Moniezia tapeworms. Our findings confirm that a problem exists regarding the occurrence of parasites of the digestive tract among sheep and goats kept under organic conditions. Therefore, correct implementation of prophylactic programmes should be emphasised to ensure the control or elimination of parasites in animals, particularly those kept on pasture.