Vaccination of all newborns with bacille Calmette-Guérin (BCG) vaccine is a standard practice in developing countries. Disseminated mycobacterial infection in an immunocompromised child can be caused by BCG and other mycobacteria. A total of 21 patients with a histopathologic diagnosis of mycobacterial infection were studied in a period of 4 years. DNA was extracted from formalin-fixed, paraffin-embedded tissues. Real-time polymerase chain reaction was performed to determine the mycobacterial species. The overall sensitivity of the assay was 71.5%. The prevalence rates of BCG, Mycobacterium tuberculosis, and other mycobacteria in the positive results were 80% (12/15), 13% (2/15), and 7% (1/15), respectively.