In the past several decades, we have made huge advances in developing techniques to investigate the genetic basis of disease. Historically, we have used linkage analysis to find causal variants for Mendelian disease with great success. More recently, we have used genome-wide association studies to begin investigating more complex traits with some success. However, more work is needed in developing methods to interpret these GWAS and identifying causal variants and their role in disease mechanism. Improving our understanding of the genetic basis of disease will us develop more effective diagnoses and treatments.