In some clinical and research settings, it is often necessary to identify the true level of “identity by descent” (IBD) between two individuals. However, as the individuals become more distantly related, it is increasingly difficult to accurately calculate this value. Consequently, we have developed a computer program that uses genome-wide SNP genotype data from related individuals to estimate the size and extent of IBD in their genomes. In addition, the software can compare a couple's IBD regions with either the autozygous regions of a relative affected by an autosomal recessive disease of unknown cause, or the IBD regions in the parents of the affected relative. It is then possible to calculate the probability of one of the couple's children suffering from the same disease. The software works by finding SNPs that exclude any possible IBD and then identifies regions that lack these SNPs, while exceeding a minimum size and number of SNPs. The accuracy of the algorithm was established by estimating the pairwise IBD between different members of a large pedigree with varying known coefficients of genetic relationship (CGR). 32:1350–1358, 2011. ©2011 Wiley Periodicals, Inc.