Micellar electrokinetic chromatography coupled to amperometric electrochemical detection was used to resolve and then quantify biogenic amines and metabolites within the fruit fly Drosophila melanogaster. A new separation scheme was devised to allow resolution of 24 compounds of interest. This was accomplished by precisely controlling the amount of base added to the background buffer, optimizing the resolution of the separation, and then calculating the pH. Here we focused on measurements of six of the analytes that are thought to be involved in the response to alcohol, dopamine, salsolinol, norsalsolinol, N-acetyloctopamine, octopamine, and N-acetyldopamine. These were identified and quantified within the fly head. We believe that the identification of salsolinol and norsalsolinol in the fly brain is novel.