There is robust evidence for heritable influences on the liability to alcohol dependence (Bierut et al., 1998). Siblings of alcohol dependent individuals have a 3–8 fold increased risk of developing alcoholism (Reich et al., 1998) with twin studies revealing the heritability of alcohol dependence to be ≈ 50% (Heath et al., 1997; Kendler et al., 1994; Knopik et al., 2004). Given its serious public health impact (Braillon and Dubois, 2005) and the strong evidence for its biological underpinnings, numerous linkage and association studies have been targeted at gene identification for alcohol dependence (Bierut et al., 2010; Edenberg and Foroud, 2006; Hill et al., 2004; Long et al., 1998; Reich et al., 1998). Recently, several genome wide association studies (GWAS) queried the genome for association (Bierut et al., 2010; Edenberg et al., 2010; Heath et al., 2011; Treutlein et al., 2009). Results surpassed genome-wide significance in one study of early-onset male alcoholics (Treutlein et al., 2009), but across the multiple efforts, effect sizes were small and did not replicate. This has generated considerable interest in the examination of other possible contributors to the “missing heritability” for alcohol dependence. One such contributor is copy number variations (CNVs).