A case of splenic abscesses caused by Paecilomyces variotii in a 21-month-old child with previously undiagnosed chronic granulomatous disease (CGD) is described. An X-linked form of CGD with deficiency of gp91-phox was diagnosed. The fungal pathogen was isolated from the abscess contents. Cure was achieved by a partial splenectomy and a prolonged fluconazole and flucytosine combination treatment regimen. P. variotii is an emerging fungus in children with CGD. Every effort should be made to recover the possible underlying immunodeficiency in children with paecilomycosis.