The goal of the present study was to assess in middle-aged rats the effects of long-term ovarian hormone deprivation on the ability of subsequent estradiol treatment to influence levels of molecular markers in hippocampus and prefrontal cortex and performance on a prefrontal cortex sensitive attention task. In initial experiments to assess estradiol effects in young adults, 2-month-old rats were ovariectomized and implanted with capsules containing cholesterol or estradiol. One set of rats was sacrificed 10 days after treatment initiation and protein levels of choline acetyltransferase (ChAT), estrogen receptors alpha (ERalpha) and beta (ERbeta), and steroid receptor coactivator-1 (SRC-1) were measured using western blotting. Another set of animals was tested on the prefrontal cortex dependent 5-choice serial reaction time task (5-CSRTT). In a second set of experiments, middle-aged rats, 10 to 12 months of age, were ovariectomized and received either cholesterol control treatment, estradiol treatment initiated immediately following ovariectomy, or estradiol treatment initiated following 5 months of ovarian hormone deprivation. ChAT, ERalpha, ERbeta and SRC-1 protein levels were assessed in one set of animals, and 5-CSRTT performance was assessed in the second set. In young animals, estradiol treatment increased levels of ChAT and ERalpha in hippocampus, and ERalpha in prefrontal cortex relative to controls. In middle-aged animals, immediate estradiol treatment significantly increased ChAT and ERalpha in hippocampus, but not prefrontal cortex. However, delayed estradiol treatment failed to significantly increase ChAT and ERalpha protein levels in hippocampus, but did so in prefrontal cortex. Levels of ERbeta and SRC-1 were unaffected by estradiol treatment in either brain area in either age group. On the 5-CSRTT, young estradiol-treated rats outperformed controls when behavior was challenged by shortening the intertrial interval (Short ITI). In the same Short ITI condition, middle-aged rats receiving immediate estradiol treatment beginning at the age of 17 months, but not 12 months, outperformed controls as well as animals receiving delayed estradiol treatment. These data indicate that prolonged ovarian hormone deprivation alters the ability of subsequent estradiol treatment to regulate ChAT and ERalpha in brain areas important for cognition, and attenuates the ability of estradiol to enhance prefrontal cortex dependent cognitive performance