Using the natural variation in histamine H(4) receptor protein sequence, we tried to identify amino acids involved in the binding of H(4) receptor agonists. To this end, we constructed a variety of chimeric human-mouse H(4) receptor proteins to localize the domain responsible for the observed pharmacological differences between human and mouse H(4) receptors in the binding of H(4) receptor agonists, such as histamine, clozapine, and VUF 8430 [S-(2-guanidylethyl)-isothiourea]. After identification of a domain between the top of transmembrane domain 4 and the top of transmembrane domain 5 as being responsible for the differences in agonist affinity between human and mouse H(4)Rs, detailed site-directed mutagenesis studies were performed. These studies identified Phe(169) in the second extracellular loop as the single amino acid responsible for the differences in agonist affinity between the human and mouse H(4)Rs. Phe(169) is part of a Phe-Phe motif, which is also present in the recently crystallized beta(2)-adrenergic receptor. These results point to an important role of the second extracellular loop in the agonist binding to the H(4) receptor and provide a molecular explanation for the species difference between human and mouse H(4) receptors.