Cotton bolls collected from fields in the Yuma Valley during 1987 and 1988 were assayed for aflatoxin on an individual basis. Distribution of aflatoxin contaminated bolls was scattered but, generally most aflatoxin occurred in the lower half of a plant. A greater proportion of pink bollworm (PBW) damaged bolls produced seed contaminated with aflatoxins than bolls not damaged and over 90% of the total aflatoxin detected was in seed produced in PBW damaged bolls. During 1988, bolls that formed early in the season contained more aflatoxin than bolls that formed later. Bolls damaged by PBW early in the season when fungal inoculum was low were infected at equal or greater frequency than bolls damaged late in the season. The results suggest that protection of early bolls from PBW damage should be a component of management programs directed towards preventing aflatoxin contamination of cottonseed.