Rats exposed to prenatal protein malnutrition are less sensitive to the amnestic effects of chlordiazepoxide when administered directly into the medial septum. Here we report that prenatal malnutrition selectively decreases gamma-aminobutyric acid A (GABA(A)) receptor gamma(2L) mRNA levels in the medial septum, consistent with malnutrition-induced decreases in the amnestic effects of chlordiazepoxide infusion. In the lateral septum, beta(2) and beta(3) mRNA levels are also decreased, suggesting that prenatal malnutrition alters GABA(A) receptor gene expression in the septal complex.