Treatment of cotton dust with sodium hydroxide in ethanol or hydrochloric acid in ethanol reduced the endotoxin contents of the treated dusts. However, only the dust treated with sodium hydroxide in ethanol reduced the pulmonary toxicity of the dust in tests with the animal model for cotton dust inhalation. In this study, bacterial lipopolysaccharide (LPS) was treated with sodium hydroxide in ethanol and hydrochloric acid in ethanol. The treated residues were derivatized with diazomethane and analyzed by capillary gas chromatography. Both treatments cleaved the fatty acid ester linkages in the LPS; the sodium hydroxide treatment was more effective than the hydrochloric acid treatment.