An 81-year-old man was admitted to the hospital with a severe sore throat and a low grade fever. A chest radiograph showed bilateral diffuse reticulonodular shadows. By fluorescent stain for mycobacteria, his sputum smear showed acid-fast bacteria. The initial polymerase chain reaction (PCR) of his sputum revealed Mycobacterium intracellulare (M. intracellulare), but not Mycobacterium tuberculosis (M. tuberculosis). However, a repeat PCR was performed because M. tuberculosis could not be ruled out due to his clinical symptoms and chest imaging. The second PCR detected both M. intracellulare and M. tuberculosis. From the standpoint of infection control, this case illustrates the possibility that M. tuberculosis could be a threat if a second PCR is not done. While PCR is a useful exam for diagnosing M. tuberculosis, it can produce false negative results. Therefore, for diagnosing tuberculosis, particularly in a case such as the present case, a second PCR, which is not normally necessary, should be done.