Sclerotia have been suggested to play a key role in the disease Cycle of Aspergillus flavus on corn. Although sclerotia are readily produced in culture by many strains of A. flavus, occurrence of sclerotia in nature has rarely been reported. Since 1987, we have repeatedly found sclerotia of A. flavus associated at low frequency (less than 10%) with A. flavus infected tight locks collected in the desert between the developing lint and pericarp, were observed on the tight lock surface after boll opening. All isolates obtained from sclerotia originating from tight locks belonged to the highly toxigenic S strain. Sclerotial production on tight locks was induced in greenhouse experiments by inoculating developing bolls through simulated pink bollworm exit holes. Sclerotia were also observed inside seeds produced in locks inoculated 28 days after flowering, during greenhouse experiments. Competitive exclusion of S strain isolates with atoxigenic L strain isolates during cotton boll infection may prevent accumulation of both aflatoxins and other toxic metabolites associated with sclerotia of A. flavus.