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Cri du Chat or 5p minus (5p−) syndrome is characterized by a deletion located on the chromosome 5 short (−p) arm and has an incidence rate of 1 in 50,000 individuals worldwide. This disease manifests in disturbances across a range of systems biochemicals. Therefore, a targeted metabolomics analysis was evaluated in patients with 5p− syndrome to help unravel the biochemical changes that occur in this disease. Urine samples were collected from people of both sexes aged 1–38 years old and analyzed by ultra‐performance liquid chromatography coupled to mass spectrometry. Student' statistical test, metabolomic pathway analysis and metabolite set enrichment analysis were applied to the data. Alterations of some amino acids and amine biogenics levels were found in Cri du Chat Syndrome individuals. The alteration of most of these metabolites is associated with energy recuperation and glycolysis. In general, we found the catabolism of some metabolic pathways to be affected in 5p− patients.