Linkage analysis is used to map genetic loci using observations on relatives. It can be applied to both major gene disorders (parametric linkage) and complex diseases (model-free or non-parametric linkage), and it can be based on either a relatively small number of microsatellite markers or a denser map of single nucleotide polymorphisms (SNPs). We describe the methods commonly used to map loci influencing disease susceptibility or a quantitative trait. Application of these methods to simulated but realistic datasets is illustrated in some detail using the program Merlin. We provide some guidance on the best methods to use in different situations and on the interpretation of output.