Cotton is the most important natural fiber used to produce apparel, home furnishings, and industrial products. Cotton fiber quality influences both manufacturing efficiency and quality of the finished products. The color, length, strength, and purity of cotton fibers all contribute to fiber quality. Cottonseed is used as food (primarily oil) and is a preferred feed for dairy cows, with dairies paying a premium for cottonseed free of aflatoxin. Modules (14,200) of seed cotton grown in South Texas from 2002 through 2008 were analyzed for fiber quality and seed aflatoxin content. Harvest date, gin date, leaf grade, and seed moisture were related with fiber quality and seed aflatoxin content. Module storage time from harvest to ginning also influenced aflatoxin contamination and fiber quality. Standard fiber quality measurements, including lint color and spot, were related with aflatoxin content and, thus, might be useful predictors of seed aflatoxin contamination. Results suggest reducing module storage time, leaf and stem impurities, and seed moisture can prevent fiber quality deterioration and reduce concentrations of aflatoxins in cottonseed.