Extensive work in recent years has suggested that a number of endogenous molecules, their derivatives or degradation products may be potent activators of the innate immune system capable of inducing pro-inflammatory cytokine production by the monocyte-macrophage system and the activation and maturation of dendritic cells. The cytokine-like effects of these endogenous molecules are mediated via Toll-like receptor (TLR) signal transduction pathways in a manner similar to pathogen-associated molecular patterns (PAMPs). However, recent evidence suggests that the reported cytokine effects of some of these putative endogenous ligands are in fact due to contaminating PAMPs. The reasons for the failure to recognize PAMP contaminants being responsible for the putative TLR ligands of these endogenous molecules include: (i) failure to use highly purified preparations free of PAMP contamination; (ii) failure to recognize the heat sensitivity of lipopolysaccharide (LPS); and (iii) failure to consider contaminant(s) other than LPS. Strategies are proposed to avoid future designation of PAMP contamination as putative endogenous ligands of TLRs.