Family, twin and adoption studies consistently suggest that genetic factors strongly influence the risk for alcohol dependence (AD). Although the literature supports the role of genetics in AD, identification of specific genes contributing to the etiology of AD has proven difficult. These difficulties are due in part to the complex set of risk factors contributing to the development of AD. These risk factors include comorbidities with other clinical diagnoses and behavioral phenotypes (e.g., major depression), physiological differences that contribute to the differences between people in their level of response to ethanol (e.g., initial sensitivity) and finally the large number of biological pathways targeted by and involved in the processing of ethanol. These complexities have probably contributed to the limited success of linkage and candidate gene association studies in finding genes underlying AD. The powerful and unbiased genome-wide association study (GWAS) offers promise in the study of complex diseases. However, due to the complexities of known risk factors, GWAS data has yet to provide consistent, replicable results. In light of these difficulties, this dissertation has five specific aims which attempt to investigate genetic risk loci for AD and related phenotypes through improved methods for candidate gene selection, analysis of a pooled genome-wide association study, genome-wide analyses of initial sensitivity and maximum alcohol consumption in a twenty-four hour period and finally, creation of a multivariate AD/internalizing phenotype.