From October 1993 to December 1995, 5 Danish freshwater rainbow trout Oncorhynchus mykiss farms were surveyed for parasites; the most comprehensive survey to date in Denmark. A total of 805 fish, aged 0+ and 1+, were examined, and the parasites were identified by light microscopy, scanning electron microscopy and histochemistry. Prevalence (protozoans and metazoans) and abundance (metazoans) were recorded. The 12 protozoans found were: an intestinal diplomonadid flagellate, the ectoparasitic kinetoplastid Ichthyobodo necator, and the ciliates Ichthyophthirius multifiliis, Chilodonella piscicola, Capriniana (Trichophrya) sp., Trichodina nigra, T. mutabilis, T. fultoni, Trichodinella epizootica, Apiosoma sp., Ambiphrya sp. and Epistylis sp. The 10 metazoan species found were: the myxosporean organism PKX, the monogeneans Gyrodactylus derjavini and G. salaris, the digeneans Diplostomum spathaceum and Tylodelphys clavata, the cestodes Proteocephalus exiguus, P. longicollis, Eubothrium crassum, and Triaenophorus nodulosus, and the crustacean Argulus foliaceus. The diplomonad occurred predominantly in anorectic undersized fish, and was associated with mortality. I. necator produced discoloration and epidermal hyperplasia and I. multifiliis infections were associated with mortalities. G. salaris and G. derjavini produced alterations (lesions and hyperplasia) of the host epidermis visible in the scanning electron microscope. Some D. spathaceum infections caused cataract. Prevalence of I. multifiliis increased with temperature (maximum at 16 to 20 degree C), whereas the diplomonad had highest prevalence at 1 to 5 degree C. Likewise, the gyrodactylids occurred more abundantly at lower temperatures.