A novel fiber optic modified thermal lens detector in combination with capillary electrophoresis (CE) is described. The probe and pump lasers used in thermal lensing were adapted via optical fibers to a commercial injection and high voltage CE system. The detector performance is demonstrated by monitoring mixtures of derivatised amino acids. Amino acids are labeled with 4-dimethylazobenzene-4-sulfonyl-chloride as absorbance reagent. Therefore all amino acids possess a large molar absorptivity in the visible region which because of its stability can be qualitatively and quantitatively detected with only one excitation line. The miniaturization of the thermal lens detector and the separation of the excitation and probe laser from the sensor head with optical waveguides permits combination with typical laboratory CE systems, which generally allow treatment of microliter volumes of amino acids.