The deorphanization of the histamine H₄ receptor (H₄R) has led to a significant number of scientific publications and patent applications. Whereas some histamine H₁, H₂ and H₃ receptor ligands were found to have significant affinity for H₄R, several agonists and antagonists with high affinity for H₄R and selectivity over the other histamine receptors were successfully designed and synthesized. Moreover, site-directed mutation studies on H₄R have been performed and reveal detailed information on receptor-ligand interactions. This review will focus on the most important H₄R ligand scaffolds and their structure-activity relationships and selectivity over other histamine receptors and specific H₄R functional activity. Experimental data are used to construct and validate high resolution three-dimensional receptor-ligand models and, vice versa, in silico models are used to design and rationalize experimental studies to probe receptor-ligand interactions.