Zygosity on multiple pregnancies is important factor of prognosis in fetus and new bones. In the past, determination of zygosity has been made mainly on the basis of histological and microscopic observations. Such a morphological distinction, however is not sufficient. Fragment analysis based on capillary electrophoresis has been developed as a rapid and accurate technique for DNA typing. To elucidate the clinical availability of fragment analysis, we examined the zygosity of nine multiple pregnancies (three twins and six triplets) by fragment analysis of microsatellite DNAs and other common DNA tests (PCR-SSCP assay and VNTR analysis using agarose gel electrophoresis). Fragment analysis and PCR-SSCP identified the heterozygosity in two of three twins and all of six triplets including one presumable dizygotic triplet, while VNTR analysis failed to recognize one of two dizygotic twins and three of five trizygotic triplets. Although detection efficiency of PCR-SSCP seems to be similar to that of fragment analysis, PCR-SSCP could not separate the several microsatellite DNAs that fragment analysis showed to be heterozygous. Moreover, fragment analysis could detect a minor population possessing the different DNA types (> 5%) in the same cell suspension. The present results suggest that fragment analysis of microsatellite DNAs may be an excellent and beneficial method for clinical application of zygosity determination in multiple pregnancies.