Background X-linked severe combined immunodeficiency (X-SCID) is a life-threatening immune disorder caused by pathogenic mutations in the IL2RG gene. We report the first patient with genetically confirmed X-SCID in Peru. Case presentation Diagnosis was suspected before patient’s birth because of family history. At birth, blood immunophenotype was compatible with X-SCID and genetic analysis revealed a pathogenic mutation in IL2RG . Intravenous immunoglobulin and antibiotic prophylaxis were initiated until patient’s referral for an available novel treatment: gene therapy. Conclusions Family background is a key point to suspect X-SCID, allowing a timely diagnosis and treatment. X-SCID requires prompt immune reconstitution. However, HSCT is frequently not available to treat newborns in developing countries.