ABSTRACT Aspergillus flavus can be divided into the S and L strains on the basis of sclerotial morphology. On average, S strain isolates produce greater quantities of aflatoxins than do L strain isolates. Sclerotia of the S strain were observed in commercial seed cotton from western Arizona. Greenhouse tests were performed to better define sclerotial formation in developing bolls. Eight S strain isolates were inoculated into developing bolls via simulated pink bollworm exit holes. All eight isolates formed sclerotia on locule surfaces, and seven of eight isolates produced sclerotia within developing seed. Boll age at inoculation influences formation of sclerotia. More sclerotia formed within bolls that were less than 31 days old at inoculation than in bolls older than 30 days at inoculation. Frequent formation of sclerotia during boll infection may both favor S strain success within cotton fields and increase toxicity of A. flavus-infected cottonseed. Atoxigenic A. flavus L strain isolate AF36 reduced formation of both sclerotia and aflatoxin when coinoculated with S strain isolates. AF36 formed no sclerotia in developing bolls and was more effective at preventing S strain isolates than L strain isolates from contaminating developing cottonseed with aflatoxins. The use of atoxigenic L strain isolates to prevent contamination through competitive exclusion may be particularly effective where S strain isolates are common. In addition to aflatoxin reduction, competitive exclusion of S strain isolates by L strain isolates may result in reduced overwintering by S strain isolates and lower toxicity resulting from sclerotial metabolites.