Determination of the sequence of the human genome has been a major undertaking. It provided powerful tools to explore the genetic component in complex diseases. To fully understand the genetic pathways contributing to complex disease traits, we must not only reveal the genomic locus of all genes involved, but also delineate the functionally relevant allelic variation in such genes and understand the patterns of gene expression leading up to the actual disease trait. Insight in the genetic contribution to clinical endpoints of complex disease and their biological risk factors, therefore, requires an understanding of both the structure and the biology of the genome. This paper constitutes a tutorial overview of the organisation of the human genome, the tools it provides for molecular genetic studies, and the genomic background of the current strategies for gene identification.