The chapter describes the use of capillary array electrophoresis (CAE) for the detection of triplet repeat expansion at the huntingtin locus associated with autosomal dominant Huntington disease (HD), an adult-onset neuro-degenerative disorder. The region of this gene that expands to disease-causing mutations consists of two adjacent tandemly repeated polymorphic triplet repeats: a diagnostic (CAG)n repeat immediately followed by a (CCG)n region. Early polymerase chain reaction (PCR)-based methods used to genotype disease-causing mutations amplified through both of the repeat regions. More accurate diagnostic risk assessment for expansion is obtained when the (CAG)n and the (CCG)n repeats are amplified separately, as well as together in a single reaction. However, these tests require three separate PCR amplifications to be run using conventional methods. The use of multicolor fluorescence detection and CAE can simplify this improved diagnostic test.