The approaches to identifying genes and genomic regions associated with human disease can be grouped into two categories: linkage analysis and genetic association analysis. Linkage analysis is useful for diseases of high penetrance that run strongly within families, but is limited in its ability to detect situations where there are multiple genes with smaller effects. An alternative is genetic association studies, which were initially performed on small numbers of candidate genes. This approach identified relatively few genes that were consistently associated with disease, but it is now possible to do a genetic association for the whole genome, making this approach more powerful. In practice, the two types of analysis are often interlinked. This article provides information on the tools needed to perform both genetic linkage and genetic association analysis.