Background: Allopregnanolone (ALLO) is a progesterone derivative that rapidly potentiates γ‐aminobutyric acidA(GABAA) receptor‐mediated inhibition and modulates symptoms of ethanol withdrawal. Because clinical and preclinical data indicate that ALLO levels are inversely related to symptoms of withdrawal, the present studies determined whether ethanol dependence and withdrawal differentially altered plasma and cortical ALLO levels in mice selectively bred for differences in ethanol withdrawal severity and determined whether the alterations in ALLO levels corresponded to a concomitant change in activity and expression of the biosynthetic enzyme 5α‐reductase.Methods: Male Withdrawal Seizure‐Prone (WSP) and ‐Resistant (WSR) mice were exposed to 72 hours ethanol vapor or air and euthanized at select times following removal from the inhalation chambers. Blood was collected for analysis of ALLO and corticosterone levels by radioimmunoassay. Dissected amygdala, hippocampus, midbrain, and cortex as well as adrenals were examined for 5α‐reductase enzyme activity and expression levels.Results: Plasma ALLO was decreased significantly only in WSP mice, and this corresponded to a decrease in adrenal 5α‐reductase expression. Cortical ALLO was decreased up to 54% in WSP mice and up to 46% in WSR mice, with a similar decrease in cortical 5α‐reductase activity during withdrawal in the lines. While cortical gene expression was significantly decreased during withdrawal in WSP mice, there was a 4‐fold increase in expression in the WSR line during withdrawal. Hippocampal 5α‐reductase activity and gene expression was decreased only in dependent WSP mice.Conclusions: These results suggest that there are line and brain regional differences in the regulation of the neurosteroid biosynthetic enzyme 5α‐reductase during ethanol dependence and withdrawal. In conjunction with the finding that WSP mice exhibit reduced sensitivity to ALLO during withdrawal, the present results are consistent with the hypothesis that genetic differences in ethanol withdrawal severity are due, in part, to modulatory effects of GABAergic neurosteroids such as ALLO.