Inflammatory substances derived from indigenous bacteria in aquatic environments or water systems are of great concern. Lipopolysaccharides (LPSs), one of the major inflammatory substances in water, are usually identified using Limurus amoebocyte lysate (LAL) assay on the basis of their endotoxic activity, but endotoxin levels do not accurately represent their inflammatory potency in humans. In this investigation, the cellular endotoxin contents of pure-cultured bacteria/cyanobacteria, which are frequently detected in water sources and distribution systems, and of indigenous bacteria in a river and in biologically activated carbon (BAC) effluent, were investigated.