Alcohol experienced during gestation is associated with the development of neurodevelopmental and neuropsychiatric dysfunctions, as well as addictive behavior in the offspring. However, the biological basis of these effects remains poorly understood. Taking into account that the extrahypothalamic corticotropin-releasing factor (CRF) system plays an important role in regulation of the negative emotional state produced by alcohol abuse and withdrawal, the present study was aimed at investigating: 1) the effect of prenatal alcohol exposure (PA) on voluntary alcohol drinking (free choice 24 hours/day) or intermittent (“drinking in the dark”) regimen in adult Wistar rats; 2) differences in the basal gene expression levels of CRF and CRF-R1 in amygdala of adult PA and control rats; and 3) the effect of voluntary alcohol drinking on the above mRNA levels. PA males displayed a significantly greater voluntary alcohol intake than control males as observed by both drinking paradigms. 24 hours after the first withdrawal episode, PA males demonstrated a higher level of anxiety in the light-dark box test. No differences were found between PA and control females. Basal amygdalar CRF and CRFR1 mRNA levels did not differ between PA and control rats of both sexes. No difference was observed in the amygdalar CRF and CRFR1 mRNA levels after alcohol drinking in PA and control males. Conversely, the CRF mRNA levels in amygdala of PA female rats decreased under the action of alcohol consumption, compared to control female rats. The results show that the PA effect on future alcohol-related behavior is sex-specific, but do not support the hypothesis that changes in CRF and CRFR1 mRNA levels in amygdala may be responsible for high alcohol intake in males.