During 1988 and 1989, counts of total viable bacteria and of viable gram negative bacteria were performed on lint and bract samples of Paymaster 404 cotton plants grown in rainout shelters. The results were compared to counts obtained from similar plants grown in open fields. In addition, the endotoxin content of both types of lint samples was determined. Samples were evaluated at boll opening, one and two weeks after boll opening and at the end of the growing season when the lint was ready to be harvested. In both years, the total and gram negative bacterial counts and the endotoxin levels of lint from the sheltered plants were significantly lower than those of lint from the open field samples. The bacterial counts of the bract tissue also was lower in samples of the sheltered plants.