A web-based application aimed at autozygosity mapping. HomozygosityMapper is independent of parameters like family structure or allele frequencies, the ‘homozygosity score’ is calculated simply from the observed homozygosity and it is robust against genotyping errors. HomozygosityMapper is much faster than conventional linkage software. The integration with GeneDistiller greatly facilitates the search for promising candidate genes compared to the conventional approach. We also encourage geneticists to consider HomozygosityMapper as a public repository for genotypes and results when publishing their homozygosity mappings. Due to its user-friendly intuitive interface and the lack of any local hardware requirements, it can be used by the geneticists themselves without the need for computer specialists.