Abstract The separation and detection of individual amyloid beta (Aβ) aggregates by capillary electrophoresis with laser-induced fluorescence detection (CE–LIF) was demonstrated. Samples were prepared with either Aβ (1–40) or Aβ (1–42) peptides and were characterized by CE with ultraviolet (UV) absorbance detection and transmission electron microscopy (TEM). Using thioflavin T (ThT) in the electrophoresis buffer, electrophoresis of aggregate-containing samples (5.0-s injection) produced up to several hundred narrow (<20ms FWHM [full width at half maximum]) fluorescence peaks. Injection of Aβ (1–40) monomer samples resulted in no additional peaks compared with controls. The CE–LIF results were validated by bulk ThT fluorescence measurements for the same samples. The potential of laser-induced fluorescence anisotropy (LIFA) with CE to characterize individual Aβ aggregates also was investigated.