We sought to characterize the interactions of an endogenous clonidine-displacing substance (CDS) with the specific receptor sites to which clonidine and its analogs bind: (a) the non-adrenergic imidazole binding site, which is present in the ventrolateral medulla (VLM) but not the frontal cortex, (b) high-affinity and (c) low-affinity states of the alpha 2-adrenergic receptor, and (d) the alpha 1-adrenergic receptor. CDS, like clonidine, potently and completely inhibited specific p-[3H]aminoclonidine binding to membranes from the VLM or from the frontal cortex. Both CDS and clonidine bound with highest affinity to imidazole binding sites in the VLM, both were 3-fold selective for high-affinity over low-affinity alpha 2-adrenergic receptors, and both exhibited lowest affinity for alpha 1-adrenergic receptors. Unlike clonidine, CDS exhibited 30-fold selectivity for imidazole over alpha 2-adrenergic receptors but showed only a weak preference for alpha 2- over alpha 1-adrenergic receptors, indicating that CDS and clonidine are not identical. We conclude that CDS is an endogenous clonidine-like substance which may be the natural ligand for imidazole binding sites in the VLM. The receptor-binding properties of CDS are consistent with the view that it is a unique and as yet unrecognized compound.