Ionotropic GABA A receptors (GABA A Rs), which mediate inhibitory neurotransmission in the central nervous system, are implicated in the behavioral effects of alcohol and alcoholism. Site-directed mutagenesis studies support the presence of discrete molecular sites involved in alcohol enhancement and, more recently, inhibition of GABA A Rs. We used Xenopus laevis oocytes to investigate the 6Ј position in the second transmembrane region of GABA A Rs as a site influencing alcohol inhibition. We asked whether modification of the 6Ј position by substitution with larger residues or methanethiol labeling [using methyl methanethiosulfonate (MMTS)] of a substituted cysteine, reduced GABA action and/or blocked further inhibition by alcohols. Labeling of the 6Ј position in either ␣2 or 2 subunits reduced responses to GABA. In addition, methanol and ethanol potentiation increased after MMTS labeling or substitution with tryptophan or methionine, consistent with elimination of an inhibitory site for these alcohols. Specific alcohols, but not the anesthetic etomidate, competed with MMTS labeling at the 6Ј position. We verified a role for the 6Ј position in previously tested ␣22 as well as more physiologically relevant ␣22␥2s GABA A Rs. Finally, we built a novel molecular model based on the invertebrate glutamate-gated chloride channel receptor, a GABA A R homolog, revealing that the 6Ј position residue faces the channel pore, and modification of this residue alters volume and polarity of the pore-facing cavity in this region. These results indicate that the 6Ј positions in both ␣2 and 2 GABA A R subunits mediate inhibition by short-chain alcohols, which is consistent with the presence of multiple counteracting sites of action for alcohols on ligand-gated ion channels.