Autozygosity mapping of recessive disorders using small numbers of highly inbred families is a powerful tool for disease gene identification. With the advent of cheap rapid methods for whole-genome SNP genotyping, data analysis, rather than laboratory work, has become rate-limiting for this approach. Here, we describe AutoSNPa, a computer program used for handling and visually presenting large amounts of SNP data, in such a way as to facilitate the rapid identification and subsequent scrutiny of autozygous regions.