Genome-wide linkage analysis is a powerful tool for the identification of genes underlying single gene and complex genetic disorders. The most commonly used technique for performing genome wide scans for genetic studies in the rat is by analysis of simple sequence length polymorphism (SSLPs) or micro satellite markers. A sensitive and flexible method for high-throughput genotyping is described. Addition of an M13 tail to the SSLP primer eliminates the need for direct conjugation of the fluorescent dye to the primers, allowing for any combination of primer and fluorophor, and therefore for easy multiplexing of primers in the same reaction. With the use of three different dyes, it is possible to run more than five hundred genotypes in each run of the automatic sequencer. Automation in the fluorescent detection system and data tracking software for processing genotypes, contributes to the ability to genotype large number of samples rapidly and accurately.