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Background: Several mutations have been described leading to impaired immunity in the IL-12/IFN-γ axis and, they confer susceptibility to mycobacterial infections. One of the more serious clinical phenotypes is secondary to mutations at IFN-γ receptor 1 gene, characterized by an early onset and more severe disease. Case report: We present a 3-month-old female patient with systemic M. tuberculosis complex who has a homozygous mutation, it affects the splicing site at IFNGR1 c.201-1G> T. At time of this report, she is with antimycobacterial treatment in the protocol of pluripotent hematopoietic cell transplantation (TCHP). Conclusion: It has been reported that antiphimic treatment should be maintained until the immune system is restored by the TCHP. If patients receive THCP before the age of 1 year old, they have a better prognosis. Diminish the levels of IFN-γ in plasma before the procedure is associated to better results.