Two independent food choice experiments were conducted in the laboratory to study the effects of four transgenic and five non-GM fungicidal wheat varieties on the food selection behaviour of the woodlouse Porcellio scaber. In general, woodlice did not avoid GM wheat as a food source and we detected no adverse effects of GM wheat on the non-target P. scaber. Moreover, we found a food preference of the woodlouse for one of the four GM varieties, Pm3b1, but not for the closely related GM Pm3b2 or for their non-GM isolines. We assume either a pleiotropic effect like lower lignin content or more suitable leaf litter coverage by microorganisms that may cause this preference and thus increasing palatability or digestibility. We discuss that this effect is ecologically not relevant.