Recently, capillary electrophoresis (CE) has been successfully used for genetic analysis instead of conventional slab gel electrophoresis. This article will give an overview of the fundamental aspects on mutation/polymorphism analyses in combination with capillary electrophoresis (CE), which mainly includes single strand conformation polymorphism analysis, denaturing gradient-gel electrophoresis, heteroduplex analysis, chemical mismatch cleavage, restriction fragment length polymorphism, allele specific oligonucleotide hybridization, allele specific amplification, primer extension, and minisatellite and microsatellite analyses. A number of key applications are summarized.