The landscape of human genetics has changed remarkably in a relatively short space of time. The field has progressed from comparatively small studies of rare genetic diseases to vast consortia based efforts that target the inherited components of common complex diseases and which typically involve thousands of individual samples. In particular, genome wide association studies have become possible as a result of a new generation of genotyping platforms. At the time of writing, these have led to the discovery of more than 150 novel susceptibility loci across a broad spectrum of diseases, a few in genes with high biological plausibility but the majority in others that had not been considered candidates. Here, we provide an overview of the field of complex disease genetics pertaining to mapping by association and consider the many pitfalls and caveats that have arisen.