GABA and glycine receptors (GlyRs) are pentameric ligand-gated ion channels that respond to the inhibitory neurotransmitters by opening a chloride-selective central pore lined with five M2 segments homologous to those of α 1 GlyR/ ARVG 2′LGIT 6′TVLTMTTQSSGSR. The activity of cyanotriphenylborate (CTB) and picrotoxinin (PTX), the best-studied blockers of the Cl − pores, depends essentially on the subunit composition of the receptors, in particular, on residues in positions 2′ and 6′ that form the pore-facing rings R 2′ and R 6′. Thus, CTB blocks α 1 and α 1/ β, but not α 2 GlyRs (Rundström, N., V. Schmieden, H. Betz, J. Bormann, and D. Langosch. 1994. Proc. Natl. Acad. Sci. U.S.A. 91:8950–8954). PTX blocks homomeric receptors ( α 1 GlyR and rat ρ 1 GABAR), but weakly antagonizes heteromeric receptors ( α 1/ β GlyR and ρ 1/ ρ 2 GABAR) (Pribilla, I., T. Takagi, D. Langosch, J. Bormann, and H. Betz. 1992. EMBO J. 11:4305–4311; Zhang D., Z. H. Pan, X. Zhang, A. D. Brideau, and S. A. Lipton. 1995. Proc. Natl. Acad. Sci. U.S.A. 92:11756–11760). Using as a template the kinked-helices model of the nicotinic acetylcholine receptor in the open state (Tikhonov, D. B., and B. S. Zhorov. 1998. Biophys. J. 74:242–255), we have built homology models of GlyRs and GABARs and calculated Monte Carlo-minimized energy profiles for the blockers pulled through the pore. The profiles have shallow minima at the wide extracellular half of the pore, a barrier at ring R 6′, and a deep minimum between rings R 6′ and R 2′ where the blockers interact with five M2s simultaneously. The star-like CTB swings necessarily on its way through ring R 6′ and its activity inversely correlates with the barrier at R 6′: Thr 6′s and Ala 2′s in α 2 GlyR confine the swinging by increasing the barrier, while Gly 2′s in α 1 GlyR and Phe 6′s in β GlyR shrink the barrier. PTX has an egg-like shape with an isopropenyl group at the elongated end and the rounded end trimmed by ether and carbonyl oxygens. In the optimal binding mode to α 1 GlyR and ρ 1 GABAR, the rounded end of PTX accepts several H-bonds from Thr 6′s, while the elongated end enters ring R 2′. The lack of H-bond donors on the side chains of Phe 6′s ( β GlyR) and Met 6′s ( ρ 2 GABAR) deteriorates the binding. The hydrophilic elongated end of picrotin does not fit the hydrophobic ring of Pro 2′s/Ala 2′s in GABARs, but fit a more hydrophilic ring with Gly 2′s in GlyRs. This analysis provides explanations for structure-activity relationships of noncompetitive agonists and predicts a narrow pore of LGICs in agreement with experimental data on the permeation of organic cations.