An experiment was set up to determine the genetic and environmental factors affecting the fatty acid composition of polar and non-polar lipids of cottonseed. Five varieties including 2 High Plains stripper types, 2 Delta picker types, and 1 Delta stripper type were chosen to evaluate the genetic variability. White flowers were tagged once a week over a four week blooming period. Developing bolls were collected every 10 days after tagging until the fruit were 50 days old. Differential extraction using hexane/ether and chloroform/methanol was used to separate the non-polar fraction from the polar fraction. The fatty acids from each fraction were methylated to form methyl esters which were analyzed by gas/liquid chromatography to define the fatty acid composition. Boll age (maturity) was the major factor affecting the fatty acid composition of non-polar and polar lipids. Week of bloom was also a significant factor. Fruit developing late in the bloom period are subject to cool temperatures in late September and October which affects their growth rate and chemical composition. Fatty acid composition of the lipid fractions differed among the varieties during the embryogenesis period (0-20 day) but not during the oil storage period (20-50 day).