Certain 3 alpha-hydroxy steroids have recently been shown to bind to the gamma-aminobutyric acid (GABA) receptor gated chloride ion channel with high affinity and to potentiate the inhibitory effects of GABA when measured both in vitro and in vivo. In the present study, a series of natural and synthetic 3 alpha-hydroxy steroids were tested for their ability to potentiate GABA-receptor-mediated chloride ion (Cl-) uptake into cerebral cortical synaptoneurosomes. The naturally occurring metabolites 3 alpha-hydroxy-5 alpha-pregnan-20-one (allopregnanolone) and 3 alpha,21-dihydroxy-5 alpha-pregnan-20-one (allotetrahydroDOC) were found to be the most active in augmenting GABAA-receptor-mediated Cl- uptake. Pharmacological activity was reduced in the corresponding isomers with the 5 beta-pregnane configuration and by some, but not all, modifications of the side chain. The ability of these steroids to potentiate muscimol-stimulated Cl- uptake is lost by acetylation at C3, introduction of unsaturation at C9(11), inversion to the 3 beta-hydroxy isomer, or inversion of configuration at C17. A facile procedure is reported for the synthesis of unlabeled and tritium-labeled allopregnanolone and allotetrahydroDOC. The 9 alpha,11 alpha,12 alpha-3H-labeled derivatives of allopregnanolone and allotetrahydroDOC were used to identify the distribution and metabolic products of these active steroids. Uptake of the more hydrophobic [3H]allopregnanolone into brain was significantly greater than that of [3H]allotetrahydroDOC. The principal 3H-labeled metabolites recovered from brain were the 3-ketone derivatives of allopregnanolone and allotetrahydroDOC, which are both inactive on GABA-receptor-mediated Cl- flux. Molecular modeling of the active steroids based on quantitative structure-activity relationships provides evidence to support the stereospecificity of the binding interactions and suggests that there may be more than one type of steroid binding site associated with the GABAA-receptor-mediated chloride ionophore.