Total bacterial concentrations and percentages of gram-negative bacteria in raw cotton were determined for samples collected from 35 cultivars and lines of cotton grown in the Brazos River Valley near College Station, Texas, in 1987. The cultivars and lines varied in levels of resistance to bacterial blight, in occurrence of mutant morphological characters (glandless, nectariless, frego-bract, okra-leaf, smooth stem, and stormproof boll), and in fiber color (white, tan, brown, and green). The morphological characters affect incidences of insect damage and boll rots, and the fiber pigments (due to tannin, lignin, and suberin) decrease enzymic degradation of polysaccharides. The cotton lines were planted on April 3, 1987, in each of four complete blocks located sequentially along the length of the field. Between initial boll opening and harvest on September 23, the cotton lint was exposed to eight rains (3.30 inches total). Analyses of variance indicated highly significant (P = 0.0001) differences in total bacteria/gm of raw fiber among cotton lines and among field blocks, and in percentages of gram-negative bacteria among cotton lines. No significant (P = 0.05) differences occurred in percentages of gram-negative bacteria among blocks. The blight resistant lines and cultivars had significantly greater numbers of bacteria/gm (1.17 million) than did the susceptible cultivars (0.99 million). Of the morphological characters, only smooth stem was associated with a significant difference in bacterial numbers. The B-smooth line had 1.48 million bacteria/gm compared to 1.14 million/gm for B-normal, a sister line. Both the brown and green fiber characters were associated with significant increases in bacteria/gm and in percentages of gram-negative bacteria; the increase associated with brown fiber also was significantly greater than that associated with green fiber. The brown fiber also contained significantly higher endotoxin concentrations than did corresponding white or green fiber. No significant changes in bacterial populations were associated with tan fiber compared to white fiber. Significant differences in bacteria/gm also occurred among cultivars with normal characters. Cultivars with high quality fiber (e.g., 'Deltapine 61', 'Acala SJ-Cl', and 'Stoneville 2131) generally had lower bacterial numbers than those with shorter, coarser fibers.