"Metabolomics", the measurement of metabolite concentrations and fluxes in cell systems, is an emerging science that has enormous potential and several unique characteristics. The current applications for this field are, primarily, toxicological profiling and biomarker studies. This review of metabolomics research highlights the identification of reliable biomarkers with emphasis on neuroAIDS. Such identification of candidate markers will be advantageous for tracking the progression of human immunodeficiency virus/central nervous system (HIV/CNS) disease to gain maximal benefit from antiretroviral treatment and to provide insight into the mechanism of related neuropathogenesis.