Parasites are important production-limiting diseases in livestock farming. Their proper treatment and control requires knowledge of their presence, epidemiology, and diagnostics. We investigated the presence of the GI parasites in pooled herd faecal samples from the islands Saaremaa (n=21), Hiiumaa (n=18), and Vormsi (n=7), collected in 2011-2012. The samples were investigated microscopically after quantitative flotation, acid-fast contrast staining for Cryptosporidium oocysts, and direct immunofluorescence for Giardia cysts. Findings included nematodes: Strongylida spp. (94.6%), Strongyloides spp. (70.7%), Trichuris spp. (9.8%); protozoans: Eimeria spp. (94.6%), Giardia spp. (69.6%), Cryptosporidium spp. (60.9%); cestodes: Moniezia spp. (22.8%); and trematodes: Dicrocoelium spp. (3.3%). E. spp. oocysts and Strongylida eggs were shed in levels that may indicate problems in some herds. The most dominant species of Eimeria was the pathogenic E. ovinoidalis (64.4%), but the other clinicallyimportant species, E. cranadallis did not dominate any samples. Based on the presented findings, it appeared that the herds had different parasitic problems needing evidence based treatments for sustainable control
