Optical genome mapping (OGM) was key for the diagnosis of a patient with mediastinal mass and pleural effusion hospitalized in an insensitive care unit at the Hospital Infantil Universitario Niño Jesús. Given the severity state of the patient, the mass could not be biopsied and the pleural effusion was extracted as part of her treatment. The analysis of cell population from pleural effusion by flow cytometry reveled a specific population CD56+CD45- compatible with a solid tumor. In order to determine the type of pediatric solid tumor, CD56+ cells were analyzed by OGM. Among the structural variants described, the interchromosomal translocation t(2;13) generating the PAX3·-FOX1 novel fusion protein was key since this translocation is a diagnostic factor for alveolar rhabdomyosarcoma. Other structural variations linked to this type of sarcoma was described such as the gain of MYCN. Once the clinical state of the patient improved, the diagnosis of an alveolar rhabdomyosarcoma was corroborated by the analysis of mediastinal mass by routine diagnosis protocols such as histopathology studies, molecular pathology analysis and FISH. Therefore, we show that OGM could be key for the diagnosis of some solid tumours in critical situations.