The GABAA ion channel protein is central to the mechanism of action of general anaesthetics and thus to the phenomenon of human consciousness. A molecular model of the alpha1beta2gamma2 gamma-aminobutyric acid type-A (GABAA) ligand-gated ion channel protein has been constructed. The cryo-electron microscopy structure of the nicotinic acetylcholine receptor (nAChR) from Torpedo marmorata and the X-ray crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis were used as starting templates for comparative modelling. Features of the modelling approach used in the development of this GABAA model include: (1) multiple sequence alignment of members of the Cys-loop superfamily; (2) the design and implementation of a quasi-ab initio loop modelling algorithm; (3) expansion of the transmembrane domain (TMD) ion pore to model the open-state of the GABAA channel; (4) hydrophobicity analysis of the TMD to refine the structure in regions involved in general anaesthetic binding. The final model of the alpha1beta2gamma2 GABAA protein agrees with available experimental data concerning general anaesthetics.