A glasshouse experiment was set up to compare processes and organisms in two soils planted with genetically modified (GM) herbicide tolerant (HT) maize treated with appropriate herbicides. This was part of a wider project (ECOGEN) looking at the consequences of GM cropping systems on soil biology using a tiered approach at laboratory, glasshouse and field scales. Soil for the experiment was taken from field sites where the same maize cultivars were grown to allow comparison between results under glasshouse and field conditions. The maize cultivars T25 (GM HT glufosinate-ammonium tolerant), Orient (non HT near isogenic control for T25) and Monumental (a conventional, non HT variety) were grown in contrasting sandy loam and clay loam soils, half were sprayed with the appropriate herbicide as used in the field and soil samples were taken at the five-leaf and flowering plant growth stage. The main effects on all measured parameters were those of soil type and plant growth stage, with four categories of subsequent interaction: (1) there were no effects of herbicide on plant growth or soil microarthropods: (2) the maize cultivar (but not the GM HT trait) had effects on the decomposition of cotton strips and the nematode community; (3) herbicide application in general altered the community level physiological profile of the microbial community and reduced both soil basal respiration and the abundance of protozoa; and (4) the specific application of glufosinate-ammonium to T25 maize altered soil microbial community structure measured by ester linked fatty acids. The results from this glasshouse experiment support the findings from the field that there are effects of herbicide application on the soil microbial and meso-faunal community but that, compared to other standard agricultural practices, the differences are relatively small.