The effects of maize (Zea mays L.), genetically modified to express the Cry1Ab protein (Bt), and an insecticide on soil microbial and faunal communities were assessed in a glasshouse experiment. Soil for the experiment was taken from field sites where the same maize cultivars were grown to allow comparison between results under glasshouse conditions with those from field trials. Plants were grown in contrasting sandy loam and clay loam soils, half were sprayed with a pyrethroid insecticide (deltamethrin) and soil samples taken at the five-leaf stage, flowering, and maturity. The main effect on all measured parameters was that of soil type and there were no effects of Bt trait or insecticide on plant growth. The Bt trait resulted in more soil nematodes and protozoa (amoebae), whereas insecticide application increased plant Bt concentration and altered nematode community structure. The only significant effects on soil microbial community structure, microarthropods, and larvae of a nontarget root-feeding Dipteran, were due to soil type and plant growth stage. The results indicate that, although there were statistically significant effects of the Bt trait on soil populations, they were small. The relative magnitude of the effect could best be judged by comparison with the insecticide treatment, which was representative of current best practice. The Bt trait had no greater effect than the insecticide treatment. Results from this glasshouse experiment were in broad agreement with conclusions from field experiments using the same plant material grown in the same soils.