Biomarkers in fish can be a useful tool for environmental monitoring of aquatic ecosystems when diffuse pollution is becoming more important and new chemicals are being created continuously. There are, however, a number of drawbacks with this method. Because of environmental variability, health status of wild fish populations may differ between years, leading to unrepresentative results in long term studies. Furthermore, genetic or adaptive differences between populations complicate the interpretation of studies on different sites. The use of farmed fish, placed in cages, can reduce these problems. However, experimental conditions are likely to differ between sites. For practical reasons it may, e.g., be neccesary to use different types of caging. Here, the use of net cages and flow through tanks has been compared for a number of biomarkers. Rainbow trout (Oncorhynchus mykiss) were placed in net cages and flow through tanks in the river Göta Alv, in western Sweden, during three different periods in 2004 and 2005. No differences between types of caging were found for any biomarker. Therefore, the results suggest that net cages and flow through tanks can be used and compared in environmental monitoring using biomarkers in caged rainbow trout. However, efforts should be taken to reduce differences in experimental conditions, e.g., light intensity and feeding levels.