Autozygosity mapping of recessive genes can be performed on a small number of affected individuals from consanguineous pedigrees. With the advent of microarray SNP analysis, acquiring genotype data has become extremely simple and quick, in comparison to gene mapping with microsatellite markers. However, the subsequent data analysis required to identify autozygous regions can still be a significant obstacle. For rapid gene identification, it may be desirable to integrate information from heterogeneous groups of affected individuals, both familial and isolated, under various assumptions of ancestry and locus heterogeneity, that are not amenable to formal linkage analysis. Unfortunately, there are few computer programs aimed specifically at facilitating this type of data sifting. Here, we demonstrate two new programs that facilitate the identification of autozygous regions within a heterogeneous SNP dataset derived from familial and sporadic affected individuals. Hum Mutat 30:1–8, 2009. © 2009 Wiley-Liss, Inc.