Developmental neurobehavioral effects associated with maternal exposure to alcohol during pregnancy are well described, but little is known about the effects of paternal exposure prior to conception. Using a quasi-experimental, within-subjects design, neurobehavioral outcomes (reflex acquisition, activity, gait) and cerebral cortical layer thickness were assessed in Sprague-Dawley rat pups from breeding pairs where the sires were exposed to alcohol. Comparisons were made on the basis of the timing of conception relative to alcohol exposure: phase 1 (controls), prior to initiation of alcohol exposure; phase 2, during the period of treatment with 20% alcohol; and phase 3, following cessation of alcohol exposure. Phase 2 and 3 pups were noted to attain negative geotaxis and reflex suspension benchmarks earlier than control pups and to have more difficulty with balance. Phase 3 pups were noted to attain righting reflex earlier than controls. In addition, phase 3 pups demonstrated increased levels of reverse maze activity and a shorter and narrower gait. Brain morphometry revealed thickening of cortical sections I-IV and V-VI resulting in overall cortical enlargement in both phase 2 and 3 pups. Further analysis of phase 2 and 3 subphases based on the presumed stages of the spermatogenic cycle during which sires were exposed to alcohol revealed significant differences in maze activity, reflex acquisition, and gait length. These findings suggest pre-conception male exposure to alcohol may have an effect on the offspring and the extent of the effects may vary with the timing of alcohol exposure relative to conception.