In humans, prenatal alcohol exposure produces long-term changes in the neural regulation of behavior including learning difficulties, attention deficits, sleep–wake disturbances, bipolar affective disorder and depression (Roebuck et al., 1999). Animal studies have yielded further details on the neurobehavioral consequences of alcohol (EtOH) exposure during critical stages of brain development. In rats, exposure to alcohol during the neonatal period, which corresponds to the third trimester equivalent in human brain development (Dobbing and Sands, 1979), induces chronic deficits on learning /memory and motor performance tasks and these behavioral manifestations are associated with alcohol-induced damage to the hippocampus and cerebellum (Goodlett et al., 1987, 1988; Kelly et al., 1988; Thomas et al., 1996, 1998). Recent applications of this animal model have revealed that circadian or 24-hour behavioral rhythmicity is also vulnerable to alcohol-induced insult during CNS development. Specifically, neonatal alcohol exposure alters fundamental properties of the activity rhythm in adult rats including its free-running period, phase-shifting responses to light and entrainment to light–dark cycles (Allen et al., 2005a,b; Farnell et al., 2004). At present, the molecular or cellular basis for these alcohol-induced disturbances in the neural regulation of rat circadian behavior is unknown. Because modifications in the molecular “gears” of the circadian clockworks produce tangible changes in the circadian regulation of behavior (Reppert and Weaver, 2002), it is possible that neonatal alcohol exposure may permanently modulate circadian properties of the rat activity rhythm by disrupting the clock mechanism perhaps through altered expression or temporal configuration of its molecular components. In mammals, the internal biological clock mediating the generation of circadian rhythms and their entrainment or synchronization to light–dark cycles is located in the suprachiasmatic nuclei (SCN) of the anterior hypothalamus. The “gears” of the molecular clockworks in the SCN consist of interlocked transcription–translation feedback loops in which the gene products of core components rhythmically regulate their own transcription or the expression of other clock genes. Clock, Period1 (Per1), Per2, Cryptochrome1 (Cry1), Cry2, and Bmal1 (Mop3) have been identified as core molecular elements of the circadian clock mechanism in the SCN based on studies demonstrating that targeted disruption or knockout of these genes in mice alters or abolishes circadian behavior (Reppert and Weaver, 2002). For example, Per1-, Per2- and Cry1-deficient mice show activity rhythms in which the free-running period is shorter than that observed in wild type animals (Bae et al., 2001; van der Horst et al., 1999; Vitaterna et al., 1999; Zheng et al., 2001). Although the SCN are essential for the generation of mammalian circadian rhythms in many biochemical, physiological, and behavioral processes, the expression and rhythmic regulation of these core clock genes are not spatially confined to the SCN. Instead, rhythmic fluctuations in the same clock genes comprising the molecular core of the SCN clockworks occur widely in other brain regions and many peripheral tissues, including the liver, heart, kidney, endocrine organs, and skeletal muscles (Shearman et al., 1997; Yamazaki et al., 2000; Zylka et al., 1998). These clock gene oscillations in other tissues are currently thought to provide for their “local” organization in time through a hierarchical system in which the SCN functions as a pacemaker linking periodic environmental cues with the internal circadian timekeeping mechanism in peripheral oscillators throughout the body. Consequently, the effects of neonatal alcohol exposure on the regulation of adult circadian behavior may be coupled with alcohol-induced changes in molecular components of the clockworks not only in the SCN pacemaker but also in peripheral oscillators. To determine whether the molecular mechanism for circadian timekeeping is vulnerable to alcohol-induced insult during the brain growth spurt, we examined the long-term impact of neonatal alcohol treatment on the temporal regulation of core clock genes in the SCN pacemaker and other brain or peripheral tissue oscillators. In this study, rats were exposed to alcohol during the neonatal period and the clock genes Per1, Per2, Cry1, Bmal1, and Rev-erbα were assessed for evidence of alcohol-induced changes in their circadian expression within the SCN, cerebellum, and liver. Because alterations in specific genetic components of the circadian clockworks have been linked to abnormal regulation of human sleep–wake cycles (Toh et al., 2001), which is a known neurobehavioral correlate of prenatal alcohol exposure in humans (Sher, 2004), information from this study may have important implications in understanding how alcohol-induced injury during rapid brain growth produces pathologies in the circadian regulation of sleep and other body processes.