Transgenic plants which produce pesticidal proteins have the potential to release these products into the soil environment when the plants are incorporated into the soil by natural or mechanical means. This could result in novel exposure of soil organims to these pesticidal proteins. There is a lack of knowledge about the fate and persistence of the transgenic pesticidal products in the soil. A model system of transgenic cotton which produces Bacillusthuringiensisdelta-endotoxin (Bt toxin) was used to address this issue. Methods were developed to quantify Bt toxin in soil and oil/plant litter by extraction of teh Bt toxin from soil with an acqueous buffer and quantification by ELISA. The highest recovery of Bt toxin from soil was obtained with a high salt, high ph buffer. In addition, for certain soil types, addition of a non-ionic detergent in the buffer were necessary to disrupt the ionic and hydrophobic interactions between the soil particles and the protein thereby allowing high recovery of the toxin. The limit of detection of this method is 0.5 ng toxin/ g soil. In laboratory settings, when transgenic cotton producing Bt toxin was incorporated into soil, the half-life of the extractable Bt toxin was two to 10 days, depending upon the experimental conditions. The method was shown to be useful in tracking over tme the persistence of both purified and transgenic Bt toxin in laboratory experiments.