A silty loam soil was incubated with the leaves and stems of two transgenic Bacillus thuringiensis (Bt) cotton varieties and nontransgenic Bt cotton to study the soil persistence of the Bt toxin from the decomposing transgenic Bt cotton tissues and its effect on soil enzyme activities. The results showed that after Bt cotton tissue amendment, Bt toxin was introduced into soil upon decomposition; about 50% of the introduced Bt toxin persisted in soil for at least 56 days. No Bt toxin was detected in the nontransgenic Bt cotton-amended soil; the amount of Bt toxin was the highest in the soil treated with the residue with the higher Bt toxin content. Activities of soil urease, acid phosphomonoesterase, invertase, and cellulase were stimulated by the addition of Bt cotton tissues, whereas activity of soil arylsulfatase was inhibited. Probably cotton tissue stimulated microbial activity in soil, and as a consequence, enzyme activities of soil were generally increased. This effect can mask any negative effect of the Bt toxin on microbial activity and thus on enzyme activities.