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 and bract samples for bacteriologic and endotoxin analyses were collected approximately twice weekly from the time of boll opening (9/20/86) until harvest (12/2/86). Total viable counts and gram negative viable counts were determined by the standard plate count method. Endotoxin analyses were performed by the Limulus amebocyte lysate (LAL) assay. Throughout the entire sampling period, approximately 95% of the bacterial flora on both the lint and the bract consisted of gram negative organisms. Bacterial counts on the lint reached a peak about twenty days after the bolls opened then declined slowly until harvest. Bacterial counts on the bract were approximately three log units higher than on the lint. Both the total and gram negative counts on the bract were fairly constant throughout the season except for a large drop at the time of the first hard frost. Then the counts increased to nearly the previous levels and declined slowly until harvest. The means of the total and gram negative counts of lint and bract taken from cotton plants which were allowed to weather in the field for an additional six weeks after harvest were approximately the same as those of the samples collected immediately before harvest. Endotoxin levels on the lint generally parallel the gram negative bacterial counts throughout the season; most of the values were between 100,000 and 200,000 ng/gm cotton. Endotoxin levels on the lint of post-harvest samples were similar to those on the lint of pre-harvest samples.