Linkage analysis is the analysis of the dependence in inheritance of genes at different genetic loci, on the basis of phenotypic observations on individuals. The methods of linkage analysis that evolved over the years 1920 to 1970 closely followed more general developments in approaches to statistical inference. In recent years, the wealth of DNA markers and the near completion of the human genome project have led to changes in approaches to linkage analysis. New computational methods have been developed to make optimal use of available multilocus marker data. With the mapping of most simple Mendelian traits and the consequent emphasis on mapping the genes contributing to more complex traits, methods involving analysis of genome identity by descnt are increasingly used. In view of the limited numbers of meioses often available for inference, fine-scale mapping and estimation of accurate meiotic maps remain open challenges. As data on genetic variation becomes available at more detailed levels, sources of variation in the processes underlying meiosis can be investigated and more accurate genetic maps obtained. Genomic data at high resolution can allow models for meiosis outcomes to be tested and more accurate models developed. These may then be used in the mapping of trait genes.