Cotton (Gossypium hirsulum) plants have been genetically modified to confer high-level resistance to damage by lepidopeteran insects. Those plants express truncated Bacillus thuringiensis (Bt) endotoxins, HD-1 or HD-73, and the antibiotic resistance selection marker protein neomycin phosphotransferase II (NPTII). Studies have been initiated to 1) estimate the amount of these proteins that will enter the environment through field planting of insect resistant cotton plants, and 2) measure their rates of degradation in soil. Levels of HD-1, HD-73 and NPTII were measured by ELISA in all major tissues collected from two lines of mature field-grown cotton plants. The Bt proteins were distributed throughout the major mature cotton plant tissues. Most of the NPTII was found only in stem tissue. A novel bioassay was developed to measure HD-1 and HD-73 degradation in soil. This assay measured tobacco budworm (lleliothia virescens) larvae mortality and/or growth inhibition due to ingestion of diet-incorporated soil samples that had been treated with the Bt proteins. These studies establish the environmental load and fate of proteins resulting from large-scale planting of insect resistant cotton.