Purpose: Childhood obesity is an increasing problem and is accompanied by metabolic disturbances. Recently, we have identified 14 serum metabolites by a metabolomics approach (FIA-MS/MS), which showed altered concentra- tions in obese children as compared to normal-weight children. Obese children demonstrated higher concentra- tions of two acylcarnitines and lower levels of three amino acids, six acyl–alkyl phosphatidylcholines, and three lys- ophosphatidylcholines. The aim of this study was to ana- lyze whether these alterations normalize in weight loss. Methods: We analyzed the changes of these 14 metabo- lites by the same metabolic kit as in our previous study in serum samples of 80 obese children with substantial weight loss (BMI-SDS reduction [0.5) and in 80 obese children with stable weight status all participating in a 1-year life- style intervention. Results: In the children without weight change, no significant changes of metabolite concentrations could be observed. In children with substantial weight loss, glutamine, methionine, the lysophosphatidylcholines LPCaC18:1, LPCaC18:2, and LPCa20:4, as well as the acyl–alkyl phosphatidylcholine PCaeC36:2 increased significantly, while the acylcarnitines C12:1 and C16:1, proline, PCaeC34:1, PCaeC34:2, PCaeC34:3, PCaeC36:3, and PCaeC38:2 did not change significantly. Conclusions: The changes of glutamine, methionine, LPCaC18:1, LPCaC18:2, LPCa20:4, and PCaeC36:2 seem to be related to the changes of dieting or exercise habits in lifestyle intervention or to be a consequence of overweight since they normalized in weight loss. Further studies should substantiate our findings.