Investigating the molecular basis of general anaesthetic activity at the GABA(A) ligand-gated ion channel is challenging due to the wide structural diversity among known general anaesthetics, and the lack of an experimental structure for the GABA(A) protein. In this molecular modelling study, two distinct binding cavities were identified within the ß(2) subunit of the transmembrane domain in a molecular model of the GABA(A) protein. The first, located near the centre of the α-helical bundle, contains Asn265 (TM2), which is essential for modulation by etomidate. The second, located near the TM1, TM3 and TM4 segments close to the membrane-extracellular interface, is capped by Met286 (TM3), a residue thought to be involved in the propofol binding site. Potential interactions of etomidate and propofol with other side-chains were also identified.