Noting the acid-conditioning effect of minocycline on the root surface, we investigated the ability of minocycline to remove endotoxin on untreated, diseased cementum in vitro. Root surface specimens affected by periodontal disease were immersed in minocycline solution (10 mg/ml, 50 micrograms/ml, and 5 micrograms/ml) for 10 minutes, 1 day, 3 days, and 7 days, and endotoxin eluted was determined by the limulus amoebocyte lysate (LAL) assay. Specimens serving as controls were treated by immersion in pyrogen-free water, agitation, polishing, or exposure to citric acid (pH 1.0) for 3 minutes. When the period of immersion was the same, the root treatment with minocycline (10 mg/ml) yielded a significantly higher rate of neutralization of endotoxin than that with a 5 micrograms/ml or 50 micrograms/ml solution. However, the detoxifying effect of this method was less adequate than that of polishing or treatment with citric acid solution. There was variability in the effects of polishing among the teeth tested. To obtain the expected effect of the root treatment with minocycline solution; i.e., removal of the endotoxin, the combining of minocycline with a mechanical root preparation, such as polishing or root planing, seems to be effective.