Paymaster 404 variety cotton was grown for this study at the Texas A&M Agricultural Experiment Station in Lubbock, Texas. Common agricultural practices were employed. Lint samples for bacteriologic and endotoxin analyses were collected twice weekly. On the first sampling day, bolls which had been tagged at the time they cracked open were collected (horizontal samples). On the second sampling day, all the bolls on plants which had a tagged boll were collected (vertical samples). Samples were collected from boll opening (9/21/87) until harvest (11/20/87). Total viable counts and gram negative Counts were determined by the Standard Plate Count Method. Endotoxin was analyzed by the LAL method. Colonization of the lint reached levels between log 6 and 7 total organisms/gm dry wt of fiber and log 5 to 6 gram negative organisms following opening of the boll. These levels were maintained until the lint was harvested. Bract supported levels of log 8 to greater than log 9 organisms throughout the season. Vertical lint samples had higher levels of both total and gram negative bacteria than their complementary horizontal samples; the opposite was found for bract samples. Throughout the sampling period, the majority of the organisms colonizing the lint and bract were gram negative. Endotoxin values were between 500 and 5000 ng/gm lint. Poor correlation was found between the endotoxin levels of samples and their numbers of viable gram negative cells.