Microsatellite polymorphisms are very important tool for linkage analysis. Now we can obtain some very fine linkage maps and many highly polymorphic microsatellite markers for linkage analysis. We developed a new efficient system for analysis of microsatellite polymorphism using automated laser fluorescent DNA sequencer. Ordinary PCR method with RI labeled primer has been used for analysis of microsatellite polymorphism, but our system mainly consists of FITC labeled primer and DNA autosequencer. There are some benefits in this system such as short analysis time, easy handling, high safety, and use of computer that enable to automatically detect allele size, save raw data, and connect to linkage analysis program on line.