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The development of capillary electrophoresis (CE) technology has been rapid over the past three years for application to the analytical separation in a variety of biopoly-mers such as proteins, polysaccharides, and
DNA
(
1
–
3
). CE offers high throughput and high resolution, automatic operation and on-line detection with automatic data acquisition, and this has stimulated its particular application to the analysis of DNA mutations for genetic analysis, and medical diagnosis. These advantages have also provided the impetus to the recent miniaturization of CE equipment to silicon-chip based devices (
3
–
12
), which provide all of the above facilities, as well as a significant improvement in the speed and degree of automation of analysis. Significant developments of other miniaturized electro-separation devices including molecular electrophoresis sieves and dielectric trapping using microelectrodes (
13
,
14
) have been described, which may be able to be integrated with CE to create micro-analytical or preparative devices. This chapter reviews the development of mutation-detection assays for use with CE.