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Magnusiomyces capitatus is an emerging opportunistic fungal pathogen particularly in immunocompromised patients. We report a case of a M. capitatus peritonitis in child with acute lymphocytic leukemia as a breakthrough infection during caspofungin therapy. The possibility of breakthrough infections caused by M. capitatus must be taken into consideration, particularly in immunosupressed patients being treated for systemic fungal infections by caspofungin. Although there are no defined breakpoints for susceptibility testing of M.capitatus, minimal inhibitory concentration results can be helpful for therapy. Antifungal treatment with amphotericin B lipid complex plus flucytosine can be effective against infections caused by M. capitatus.