An important aspect of the risk assessment of pesticidal transgenic plants is the potential for detrimental effects on the soil ecosystem from residual plant material following harvesting and tillage. We evaluated this concern by placing leaves of three different lines of cotton genetically engineered to produce the Bacillus thuringiensis var. kurstaki (B.t.k.) endotoxin in soil and monitoring numbers and species of indigenous soil bacteria and fungi. Four experiments, lasting 28 or 56 days, were performed using combinations of the following treatments: (1) soil only; (2) soil + purified B.t.k. toxin; (3) soil + parental cotton; (4) soil + purified B.t.k. toxin + parental cotton; (5) soil + B.t.k. toxin-producing cotton. Two of the three transgenic cotton lines caused a transient increase in total bacterial and fungal population levels that was significantly higher on several sample days in the experiments than the levels in the other treatments. In contrast, neither the third transgenic cotton line nor the purified B.t.k. toxins had any significant effects on the total numbers of bacteria and fungi. Transient changes in bacterial species composition, measured by biochemical tests of individual cultures, community substrate utilization and DNA fingerprinting, were also observed in treatments with the two transgenic plant lines. The plant line specificity of the response, and the lack of effects from the purified B.t.k. toxins, suggest that the observed effects of the two transgenic plant lines on soil microorganisms may not have resulted from the plants' production of B.t.k. toxin. We suggest that genetic manipulation or tissue culturing of the plants may have produced a change in plant characteristics, aside from B.t.k. toxin production, that can influence growth and species composition of soil microorganisms.