The prevalence of Cryptosporidium and Giardia was studied on 10 intensively reared sheep and goat farms in the province of East Flanders, Belgium. Random faecal samples were collected and examined using the Merifluor((R)) immunofluorescence assay. Cryptosporidium positive samples were withheld for molecular identification using primers targeting the 18S rDNA, 70 kDa heat shock protein and 60 kDa glycoprotein gene. For the molecular identification of Giardia the beta-giardin gene and a recently developed assemblage specific PCR based on the triose phosphate isomerase gene were used. The prevalence of Cryptosporidium in lambs was 13.1% (18/137), on 4 out of 10 farms. In goat kids the Cryptosporidium prevalence was 9.5% (14/148), on 6 out of 10 farms. The molecular characterisation of Cryptosporidium positive isolates indicated that in lambs (n=10) the cervine genotype was predominant, whereas in the goat kids (n=11) only C. parvum was identified, with subgenotypes IIaA15G2R1 and IIdA22G1. The Giardia prevalence was 25.5% (35/137) in lambs with all 10 farms being positive, and 35.8% (53/148) in goat kids with 8 out of the 10 farms being positive. Both in the goat kids and in the lambs the host specific assemblage E was most commonly identified. However, the zoonotic assemblage A was identified in 6 out of 28 goat kids and in 2 out of 8 lambs, based on the beta-giardin sequence alignment. Using the assemblage specific PCR, mixed assemblage A and E infections were additionally identified in 2 lambs and in 5 goat kids. The results of the present study indicate that both Cryptosporidium and Giardia are common parasites on intensively reared sheep and goat farms in the province of East Flanders, Belgium, and that they are a potential source for zoonotic infections.