Micellar electrokinetic capillary chromatography with electrochemical detection has been used to quantify biogenic amines in freeze-dried brains of Drosophila melanogaster. Freeze-drying samples offers a way to preserve the biological sample while making dissection of these tiny samples easier and faster. Fly samples were extracted in cold acetone and dried in a rotary evaporator. Extraction and drying times were optimized in order to avoid contamination by red pigment from the fly eyes and still have intact brain structures. Single freeze-dried fly brain samples were found to produce representative electropherograms as a single hand-dissected brain sample. With utilization of the faster dissection time that freeze-drying affords, the number of brains in a fixed homogenate volume can be increased to concentrate the sample. Thus, concentrated brain samples containing five or fifteen preserved brains were analyzed for their neurotransmitter content, and four analytes; N-acetyloctopamine, N-acetylserotonin, N-acetyltyramine, and N-acetyldopamine were found to correspond well with previously reported values.