A capillary electrophoresis method has been developed for the analysis of melatonin, which depends on whether tryptamine and serotonin must be determined as well. If only a melatonin analysis is required, a bare capillary with a pH 4.41 buffer separates the analyte from the other two compounds, which are unresolved. If determination of all three species is necessary, a bare capillary with a pH 2.14 buffer is used. For better resolution of tryptamine and serotonin without the analysis of melatonin, a chemically modified capillary surface that lowers the electroosmotic flow is necessary.