To obtain information both about the prevalence of Giardia and Cryptosporidium in Danish cattle and pigs as well as the possible influence of different management systems on the occurrence and intensity of infection, we conducted an epidemiological survey comprising 50 randomly selected dairy and sow herds, respectively. Each herd was visited once for the collection of faecal samples and registration of basic management parameters. Faecal samples were collected from three different age groups of animals, i.e. 5 sows/cows. 10 nursing piglets/calves less than 1 month, and 10 weaner pigs 8-45 kg/calves 1-12 months. The faecal samples were purified and the number of (oo)cysts quantified. The study revealed an age-specific herd prevalence of Cryptosporidium of 16, 31 and 100% for sows, piglets and weaners, respectively, and of 14, 96 and 84% for cows, young calves and older calves, respectively. For Giardia the age-specific herd prevalence was 18, 22 and 84% for the sows, piglets and weaners, while for cattle herds the prevalence was 60, 82 and 100% for cows, young calves and older calves, correspondingly. The (oo)cyst excretion levels varied considerably both within and between herds for all age groups. Risk factors were evaluated by using proportional odds models with (oo)cyst excretion levels divided into four categories as response. Among the numerous risk factors examined, only a few were demonstrated to have a statistically significant influence, e.g. the use of an empty period in the calf pen between introduction of calves for both parasites had a protective effect in young calves. For weaners, use of straw in the pen and high pressure cleaning between batches of weaners had a preventive effect against higher Cryptosporidium oocyst excretion levels.