The metabolic study of an organism may make it possible to monitor, through the metabolites, the physiology and/or pathology of the organism itself. Metabolomics, in the strictest sense, "the set of metabolites, the final products of the genetic expression". Most clinical chemistry tests available today rely on old technologies that measure only a single chemical in blood, urine or other biofluids, and these tests are neither sensitive nor specific for any particular disease. Metabolomics offers a holistic approach to systems medicine, with the promise to enhance clinical chemistry diagnostics in several pathologic conditions. The present review covers the application of clinical metabolomics in three different areas of respiratory diseases in pediatrics: asthma, pneumonia and bronchiolitis. Comparison between two 1H-NMR urine spectra by two bronchiolitis patients are also presented.