Eimeria and Cryptosporidium are among the most common bovine parasites in the world, but little is known about them in Estonia. Basic field research is needed to gain insight into pathogen dynamics, providing knowledge for veterinarians and research. A survey of 45 Estonian dairy farms in 15 counties was carried out between 2006 and 2007. Three age groups: <3, 3-12, and >12 months old animals were sampled. Collected faeces were examined by quantitative flotation and Ziehl-Neelsen contrast staining, and species examined morphologically. Selected samples containing Cryptosporidium were additionally examined by polymerase-chain-reaction (PCR) and sequencing to determine genotypes. Twelve species of Eimeria were identified, seven previously unknown in Estonia. Main species in samples were E. bovis (30%), E. zuernii (23%), and E. ellipsoidalis (14%). All herds were infected and animals aged 3-12 months were more commonly infected with Eimeria oocysts (63%) than any other group. Calves <3 months shed most oocyst, but high counts were rare. A negative association (slope=-0.16, p<0.001) was found between the number of animals infected with Eimeria and the age category. Cryptosporidium were detected in 84% of the farms, and C. andersoni and C. parvum were successfully identified. Though prevalences of Cryptosporidium in the age groups were similar to the sample prevalence (30%) an increase in the infections was found with increasing age (p<0.001). Higher diarrhoea scores were negatively associated with Eimeria spp. infection (slope=-0.08, p<0.05), whereas Cryptosporidium could not be associated with the presence of diarrhoea. Frequent low intensity infections of animals in all age groups with both parasites apply a constant stress on the animals with impact on health and production. The Estonian results are different compared to available studies in regard of: older animals commonly being infected, finding of modest oocyst counts, and distribution of Eimeria species.