Botanical and microbial analyses on 70 raw cottons from seven U.S. cotton growing regions or subregions were performed. All trash particles greater than 50 micrometers were removed manually and were identified microscopically. Endotoxins in plant components were estimated by a modified microtiter technique for the Limulus polyphemus amoebocyte lysate test. Cottons from poorer grades contained greater amounts of bract leaf, total botanical trash, and stained leaf than higher grade cottons. The average number of gram negative bacteria (GNB) in bract leaf, stem, seed, bark, stained lint and clean lint was 6.38, 5.65, 5.83, 6.14, 6.30, and 4.92 log N/gram, and the average endotoxin for these components was 3.67, 3.52, 3.29, 3.97, 4.01 and 2.97 log nanogram/gram. Bract leaf, seed, and cleaned lint from strict middling cotton contained significantly less endotoxin than poorer grades. Cotton components from the far west contained lesser amounts of endotoxin than those from other regions. There was no significant difference in botanical trash and stained lint between different regions. The authors conclude that the regional differences could not be ascribed to botanical composition and that climatic variables and harvesting time may be the cause of GNB and endotoxin variation.