Endotoxin is a relatively stable material, but there have been no definitive observations regarding the stability of endotoxin in cotton dust samples stored over prolonged periods of time. Subsets of vertical elutriator cotton dust samples obtained by carding a single blend of cotton and sampling airborne dust in the USDA model cardroom and remote room were, assayed for endotoxin at three times--several weeks, three years, and six years after dust collection. Personnel performing the assays were blinded to the identity of the samples at the second and third time points. Results from remote room samples suggest that endotoxin concentration was not affected by storage over the six-year time period. Results from the cardroom samples suggest that endotoxin concentration diminished over time, but this may be an artifact of the procedures used, rather than an actual decline in the endotoxin concentration in the dust. A possible explanation for this discrepancy and procedures to avoid it are presented.