Genome-wide association studies and, more recently, next-generation sequencing studies have accelerated the investigation of complex human traits by providing a wealth of association data linking genetic variants to diseases and other phenotypic traits. These data promise to transform our understanding of the molecular pathways underlying complex human traits, but only if functional evaluation of the novel genetic variants is undertaken. Here, we review recent examples in which such functional evaluation has been attempted, with varying degrees of success, and we highlight new technological advances that should greatly enhance our ability to identify and dissect causal genotype-phenotype relationships.