Venom of snakes from the Elapidae and Hydrophyidae families possesses a complex mixture of toxin proteins with pronounced pharmacological activities. Some of these proteins are neurotoxins, whereas others are potent cardiotoxins. Neurotoxins bind specifically to the nicotinic acetylcholine receptor and block synaptic nerve transmission. The short and long neurotoxins exhibit sequence homology and share a common global fold. They all consist of three finger like loops protruding from a globular core region cross-linked by disulfide bonds. The α-neurotoxins have been used as tools for the isolation and characterization of the nicotinic acetylcholine receptor (nAChR). Binding of toxin to the nAChR mostly involves residues from loops I and II, with a smaller contribution from loop III. The neurotoxins are supposed to bind with the nAChR through charge-charge interaction between the base residues of neurotoxins and acidic residues of nAChR, and the central loop of the toxin plays an important role in its binding ability to the receptor. Recently, a natural homologue of the extracellular domain of the nAChR, the acetylcholine-binding protein (AChBP) was discovered. It makes it possible to position the toxin molecule on AChBP and elucidate an experimentally based three-dimensional model of toxin-receptor complex. The modes of binding of short and long neurotoxins to the acetylcholine receptor are believed to be significantly different, but both toxins have a common binding site on the α-7 subunit of the acetylcholine receptor (AChR), spanning residues 182–206.Cobrotoxin is a neurotoxin protein isolated from Formosan cobra, Naja naja atra. Several groups have worked to elucidate the structure and functional relationships of cobrotoxin by chemical modification studies. Due to the great pharmaceutical applications of cobrotoxin our group has focused on this area of research. We have successfully cloned and overexpressed the cobrotoxin in high yields in soluble state and structure-activity relationships were monitored by the HSQC (Heteronuclear Single-Quantam Coherence) spectrum of recombinant cobrotoxin titrated with a peptide derived from Torpedo nAChR. In this review we describe structure and functional relationships of cobrotoxin with chemical modifications and nuclear magnetic resonance (NMR) studies. These studies have defined the nAChR binding sites on cobrotoxin, and given clues to design of drugs that target the nicotinic pharmacopoeia.