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. Hum Mutat 27(10), 1041–1046, 2006. © 2006 Wiley‐Liss, Inc.