The treatment of multidrug-resistant tuberculosis (TB) requires the use, for long periods, of drugs liable to cause significant side effects. In the case of misdiagnosis of multidrug-resistant TB, the patient is exposed to toxic substances without any benefit. In low-income countries, where the microbiological diagnosis of TB relies on microscopy only, the misdiagnosis of multidrug-resistant TB is very frequent in patients persistently smear-positive despite anti-TB treatment, with the possibility of an infection due to non-tuberculous mycobacteria (NTM) being neglected. The isolation of a mycobacterium from the sputum of a Somali patient apparently confirmed the previous diagnosis of cavitary pulmonary disease. Preliminary investigations led, at first, to the strain being identified as multidrug-resistant Mycobacterium tuberculosis, with findings fully in agreement with the patient's history, which was characterized by repeated interruptions of anti-TB treatment. Thorough phenotypic and genotypic analyses led subsequently to the recognition that the strain was a previously unreported non-tuberculous mycobacterium. The patient, who was unresponsive to the anti-TB treatment, dramatically improved once a drug combination active against NTM was used. A major objective of this article is to alert the medical community to the risk, present also in settings in which sophisticated diagnostic techniques are used, that a cavitary infection due to NTM, and consequently not responding to the anti-TB standard regimen, will be mistaken for multidrug-resistant TB.