A liquid chromatography method coupled with electrochemical detection has been developed for the direct measurement 5-hydroxytryptamine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) in brain microdialysates. The separation conditions have been optimized to detect only the 5-HT and 5-HIAA in dialysates and elute the other monoamines and their metabolites in the void. Linear regression analysis of chromatographic peak area as a function of concentration in the range 5-1000 pg/mL gave correlation coefficients over 0.995. Sample stability and an assay validation for precision and accuracy were also performed. The limit of detection (S/N = 3) for 5-HT was 12 femtomol/mL. The method has been applied to simultaneously measure extracellular 5-HT and 5-HIAA in brain microdialysates from the pineal gland and caudate-putamen of awake and freely-moving rats under basal conditions.