A practical capillary array electrophoresis sequencer has been constructed and tested for large scale DNA sequencing. This system employs a scanning confocal optical system to detect DNA fragments electrophoresed on a capillary array. By using the recently developed energy transfer fluorescent primers, sensitive four-color detection is facilitated while exciting with just a single laser wavelength (488 nm) from an argon ion laser. Software for facile reduction of the images to four-color trace files and for automated base-calling have also been developed. This system can detect up to 25 capillaries at a time and has a raw sequencing rate of approximately 6 kilobases/hour. Applications to mitochondrial D-loop DNA sequencing are presented as a demonstration.