Small insertions or deletions (InDels) constitute a ubiquituous class of sequence polymorphisms found in eukaryotic genomes. Here, we present an automated high-throughput genotyping method that relies on the detection of fragment-length polymorphisms (FLPs) caused by InDels. The protocol utilizes standard sequencers and genotyping software. We have established genome-wide FLP maps for both Caenorhabditis elegans and Drosophila melanogaster that facilitate genetic mapping with a minimum of manual input and at comparatively low cost.For humans and model organisms, such as worms and flies, the availability of high-density sequence polymorphism maps greatly facilitates the rapid mapping and cloning of genes [1-3]. Key advantages of most molecular polymorphisms are the fact that they are codominant and in general phenotypically neutral. The vast majority of sequence polymorphisms are single-nucleotide polymorphisms

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