Rhabdomyosarcoma (RMS) is a type of soft tissue sarcoma that mainly occurs in children. RMS can be divided into two subtypes embryonal (ERMS) and alveolar (ARMS). The ARMS subtype can be especially aggressive when a balanced chromosomal translocation is present. This translocation results in the expression of a PAX3/7-FOXO1 fusion protein, an oncogenic transcription factor. PAX3-FOXO1 positive RMS has an especially bad prognosis and survival rate. In the cell painting assay relevant organelles are stained and morphological features are extracted on a cellular level. Based on these features, morphological profiles of each cell type and a similarity score can be calculated. The morphological profiles of ERMS cell lines RD and RD18 as well as the ARMS cell lines RH30 and CW9019 were obtained. RD and RD18 are most similar to each other followed by RH30. CW9019 has a very different profile from the other cell lines. Since ERMS is associated with a better survival rate a drug that reprograms the phenotype from ARMS to a more ERMS-like phenotype might sensitize the cells to the standard treatment of RMS. ARMS patients might then benefit from a combination therapy of such a drug and the standard treatment. To find such a drug a drug screen was conducted. Drugs were selected for the screen that either target fusion-protein stability or overexpressed targets of the fusion protein. Phenotypic reference compounds were included to get a first idea of the mechanisms and involved organelles of the screened drugs. In total, 30 compounds and 9 phenotypic reference compounds were screened for changing morphological profiles of RMS cell lines with the cell painting assay. 15 compounds were identified that change the phenotype of the ARMS cell line RH30. In addition, 7 of these compounds shift the phenotype of RH30 towards an ERMS-like phenotype. If that morphological resemblance of RH30 cells to ERMS cells translates into a change of a more ERMS-like behavior and sensitizes the cells for the standard treatment of RMS remains to be investigated. The reprogramming hits showed high similarity with phenotypic reference compounds that increase nucleus size which might suggest changed behavior of the fusion protein. Especially, Bosutinib, Midostaurin and Alisertib are promising new compounds for ARMS treatment. They shifted the ARMS phenotype towards an ERMS-like phenotype in the drug screen. This shift is likely a result of the interaction with PLK1 or Aurora-kinase A that are shown to have an influence on fusion-protein stability.