A parasitological investigation of Danish farmed freshwater (180 fish) and marine rainbow trout (170 fish), Oncorhynchus mykiss, was performed with an emphasis on the occurrence of zoonotic parasites. Reliability of the parasitological methods applied was assessed by examining fish from a stock of wild Atlantic cod Gadus morhua caught in the Sound (Øresund). While wild fish carried a number of zoonotic parasites, we found that farmed fish, both in the fresh and marine environment, were free of these parasites. Non-zoonotic trout parasites found were eye-flukes Diplostomum paracaudum, D. pseudospathaceum and Eubothrium crassum in maricultured rainbow trout. The acanthocephalan Echinorhynchus truttae and Diplostomum sp. were found in freshwater trout. In contrast, wild cod were infected with five different nematode species (Anisakis simplex, Contracaecum osculatum, Pseudoterranova decipiens, Hysterothylacium aduncum, Cucullanus cirratus), three trematode species (Lepidapedon elongatum, Cryptocotyle lingua, Hemiurus communis), one copepod species (Lernaeocera branchialis) and one myxozoan (Myxobolus aeglefini). The risk factors associated with aquaculture production in an infectious aquatic environment are analyzed and reasons for absence of zoonotic parasites in aquacultured trout are pinpointed. Based on the analysis recommendations for management practices securing parasite freedom in aquacultured fish are given.