Our ability to map and sequence whole genomes is one of the most important developments in biological science. It will provide us with an unprecedented insight into the genetic background of phenotypic traits, such as disease resistance, reproduction and growth and also makes it feasible to study the processes of genome evolution. The main focus of this thesis has been to develop a linkage map of the horse (Equus caballus) genome. A secondary aim was to expand the number of physically mapped genes in the horse, allowing comparative analyses with data from the human genome map. Finally, attempts were made to identify single nucleotide polymorphisms (SNPs) on the horse Y chromosome. The development of a genome map relies on the information generated by both linkage and cytogenetical studies. To integrate genetical and physical assignments in the very early phase of equine genome map construction, 19 polymorphic microsatellite markers were isolated from lambda phage clones which, in parallel, were physically assigned to chromosomes by fluorescent in situ hybridization (FISH). The microsatellites were simultaneously mapped by linkage analysis in a Swedish reference pedigree. A first primary male autosomal linkage map of the domestic horse was constructed by segregation analysis of 140 genetic markers within eight half-sib families with, in total, 263 offspring. One hundred markers were arranged into 25 linkage groups, 22 of which could be assigned physically to 18 different chromosomes. The total map distance contained within linkage groups was 679 cM. The presented map provides an important framework for future genome mapping in the horse. Our contribution to the comparative horse genome map, was the presentation of map data for 12 novel genes using FISH and somatic cell hybrid mapping. AD chromosomal assignments except one were in agreement with human-horse Zoo-FISH data. The exception concerned the CLU gene which was mapped by synteny to ECA2 while human-horse Zoo-FISH data predicted that it would be located on ECA9. The level of SNPs on the horse Y chromosome was also investigated by DNA sequencing and denaturing high performance liquid chromatography (DHPLC) of Y chromosome-specific fragments derived mainly from BAC clone subcloning. The amount of genetic variability was found to be very low, consistent with low male effective population size.