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Background: Bacille Calmette-Guerin (BCG) is included in the routine vaccination program in Gaza and the West Bank. Although safe, complications can occur and include local, extra-regional and disseminated BCG infection. Therefore it is contraindicated in immunodeficiencies. However, most infants are immunized prior to diagnosis of immunodeficiency. We report clinical and immunological characteristics of patients referred with severe combined immunodeficiency (SCID) who suffered from BCG complications. Methods: Files of patients referred for evaluation of immunodeficiency from January 2008 to February 2016 were retrieved. All patients have received BCG. Cell surface markers of peripheral blood mononuclear cells (PBMCs) were measured by immunofluorescent staining and flow cytometry. Serum concentrations of immunoglobulins were measured using nephelometry. Genetic diagnosis of SCID was made by direct Sanger sequencing of candidate genes. BCG complications were classified as: a) local; b) regional; c) distant; and d) disseminated disease. Results: Twenty-one children were diagnosed with SCID. BCG complications were diagnosed in 12 (57.1%). Eight patients developed local and regional disease (67%) and 4 (33%) had disseminated infection. Patients received at least three drugs: isoniazid, ethambutol and rifampicin. Outcome was relatively favorable with eight patients surviving (66.6%). No death related to BCG infection was observed. Disseminated disease was associated with reduced numbers of total lymphocytes, CD3 and CD8 levels ( p < . 05). Conclusions: Although high rates of BCG complications were observed, mortality was not increased and outcomes were good. Increased awareness in countries where BCG vaccine is not routinely administered and newborn screening programs for SCID could reduce complication rates.