Capillary electrophoresis (CE) is a highly efficient separation method and used for separation of many compounds. We developed a fast and sensitive analytical method for β-amyloid (Aβ) aggregates by the combination of CE-laser-induced fluorescence and a fluorescence reagent, thioflavine T. The developed method is also applicable to a high-throughput screening of Aβ aggregation inhibitors, which are expected to be an effective therapeutic agent candidates of Alzheimer’s disease.