We report the first description of visceral leishmaniasis (VL) infection as a harbinger of chronic granulomatous disease (CGD) in a 3-year old child. Although VL is not frequently suspected in CGD patients, our case emphasises the importance of a complete evaluation of the immune system in children presenting with VL in order to exclude underlying immunodeficiency states. As the prognosis of CGD is poor, with high morbidity and mortality, establishing an early diagnosis has important practical implications in the successful treatment of these patients. Following the diagnosis, the patient received Human Leukocyte Antigen (HLA) identical sibling bone marrow transplantation (BMT). The child is now 2 years post-transplant and is in good general conditions with normal blood counts, and evidence of full-donor chimerism in repeated fluorescence in situ hybridization (FISH) studies.