Fluorescence detection of oligonucleotide fragments produced by the dideoxy method. A sequencing reaction is performed with four chain-terminating dideoxy nucleotides, each labeled with a tag that fluoresces at a different wavelength. The color of each fragment indicates the identity of the last base in the chain. The fragments are separated by size using capillary electrophoresis and the fluorescence at each of the four wavelengths indicates the sequence of the complement of the original DNA template.