Mycobacterium genavense is recognized as a life-threatening pathogen in severely immunocompromised patients, mostly in those with advanced human immunodeficiency virus infection. We report a case of M. genavense infection in a lung-transplant recipient with late-onset death occurring from disseminated infection. In human immunodeficiency virus-negative patients, there exist only about 10 reports of disseminated M. genavense infection in immunocompromised hosts; and to our knowledge, this is a first reported case of M. genavense infection after a lung transplant. Diagnosis of M. genavense was obtained only with nucleic acid-based identification technique, as frequently observed in a few cases of human immunodeficiency virus-negative patients. A striking feature was the recurrence of this infection in our patient after a seemingly infection-free period of 3 years. Because M. genavense infection can be life-threatening, clinicians must be aware of the frequent requirement for nucleic-acid-based identification for its diagnosis.