Cotton lint can be naturally contaminated with bacterial endotoxins in the field prior to harvest, and bacterial endotoxins have been found in cotton dust from textile mills. Correlations between endotoxin levels and declines in pulmonary function in human volunteers exposed to airborne cotton dust have been reported. A microbiological field study was organized by Cotton Incorporated in 1986 to study the dynamics of cotton lint contamination by bacteria and their endotoxins throughout the harvest season in four growing locations. Chemical components on the cotton lint may determine or be affected by microbial growth. Simple organic plant acids and sugars were extracted from the lint with water. The extracts were freeze-dried, derivatized, and analyzed by capillary gas chromatography. Levels of organic acids and sugars were far greater in cotton lint samples from California than those from Texas. In all locations, the levels of acids and sugars present on the fiber decreased throughout the harvest season. For the Texas and Mississippi growing locations, chromatographic profiles from the late harvest samples were qualitatively different from those of the early harvest samples.