The amino acid neurotransmitters gamma-aminobutyric acid (GABA) and glutamate have been implicated in mood disorders and high performance liquid chromatography (HPLC) is an important method in their quantitation. This paper describes a method which employs either electrochemical or fluorescent detection of the amino acid derivatives formed by a reaction with naphthalene-2,3-dicarboxaldehyde (NDA) in the presence of cyanide ions. Elution is based on an isocratic protocol and is achieved in 20 min or less. The method is reproducible, shows excellent linearity and generates derivatives which are stable for up to 16 h. Successful application of the method to a maternal deprivation study has identified the hippocampus and the brainstem as possible sites of long-term alteration in this paradigm.