Nicotinic acetylcholine receptors (nAChRs) display a broad variety of subtypes, which in turn present a complex subcellular and regional expression pattern in the brain, as well as a specific pharmacological profile. The association of these nAChRs with different types of brain disease has turned them into interesting drug targets for the treatment of Alzheimer's disease or schizophrenia, or for anti-smoking compounds among others. In the same way, muscle-type nAChRs present at neuromuscular junctions are also being targeted by muscle relaxants. However, to date no high-resolution structural data are available on functional pentameric forms of membrane-bound nicotinic receptors. Therefore, characterization of the selectivity profiles of different nicotinic receptor subtypes, enabling efficient drug design, is a serious issue. Over the last eight years various high-resolution structures of acetylcholine binding protein (AChBP), which is homologous to the extracellular ligand-binding domain of the nicotinic acetylcholine receptor, have been obtained. AChBPs in complex with different ligands have provided detailed insight into the neurotransmitter binding site of nicotinic acetylcholine receptors. We present here the various efforts towards rationalizing subtype specificity in these receptors through the structural studies of acetylcholine binding protein-ligand complexes.