Transgenic cottons expressing the insecticidal proteins of Bacillus thuringiensis (Bt) have been widely adopted by cotton producers throughout the USA to control lepidopteran pests. Beginning in 1999, a five year study was conducted in Arizona, USA to examine the comparative effects of Bt cotton on non-target organisms, with special emphasis on natural enemy abundance and the community function of the natural enemy complex. Univariate and multivariate methods were used to examine effects on individual species and on the natural enemy complex as a whole. Combined analyses over all years indicate that the abundance of several natural enemy taxa, including some spiders, Hippodamia convergens, Geocoris punctipes, Nabis alternatus and Drapetis nr. divergens were significantly reduced in Bt cotton compared with non-Bt cotton. In all cases, population reductions were generall less than 10%. However, the overall function of the natural enemy community, measured as rates of predation and parasitism on two key pests (Pectinophora gossypiella and Bemisia tabaci) of cotton in the western USA were unaffected in Bt cotton. Retrospective statistical power analyses were conducted to define the resolution of the experimental design to detect treatment differences.