Introduction: Non-tuberculous mycobacterial lung diseases (NTMLD) occur rarely and are diagnosed mainly in patients belonging to risk groups. Pulmonary hypertension (PH) has not been recognised as a risk factor for NTMLD yet. The aim of the study was to analyse the clinical course and predisposing factors of NTMLD recognised in our centre between 2002 and 2012 in patients with chronic thromboembolic pulmonary hypertension (CTEPH) and idiopathic pulmonary arterial hypertension (IPAH). Material and Methods: Thirteen patients (10—CTEPH, 3—IPAH) entered the study. PH was recognised during right heart catheterisation. Median value of mean pulmonary artery pressure (mPAP) was 49 mm Hg (39–65 mm Hg). NTMLD was diagnosed according to ATS guidelines (2007). Results: M. kansasii was the most frequent pathogen. Most patients complained of the exaggeration of dyspnoea and productive cough. Computed tomography of the chest with angiography revealed infiltrations with cavitation in seven patients and cavities surrounded by micronodules in six patients. In all CTEPH patients, NTMLD developed in the hypoperfused lung areas. No parenchymal abnormalities preceded the development of NTMLD. After diagnosis all of the patients received antituberculous treatment; in 12/13 improvement was achieved. By the end of March 2014 seven patients died due to right heart insufficiency, no deaths due to NTMLD were noted. Conclusions: NTMLD should be suspected in patients with CTEPH or IPAH, presenting with productive cough and a new pulmonary infiltrate with cavitation. In patients with CTEPH, special attention should be paid to a new cavitary lesions without accompanying thrombus in the artery supplying the area. High mPAP (CTEPH/IPAH) and hypoperfusion (CTEPH) are predisposing to NTMLD.