Rainbow trout (Oncorhynchus mykiss) is the dominant fish species in Danish freshwater aquaculture and the annual production is about 30.000 tonnes. Only a minor part of this production is organic, but the proportion of farmed organic rainbow trout is continuously increasing. The aim of the project OPTIFISH has been to elucidate the effect of diet ingredients on fish health. Diets with either organic or non-organic ingredients were compared. The OPTIFISH project has shown that the ingredient type in the diet is more important for the bacterial intestinal microbiota of the fish than if the diet ingredients are of organic or conventional origin. Furthermore, fish fed organic diets appear to acquire the same health status as fish fed conventional diets.