Whipple's disease (WD) is a multiple-system chronic disease caused by
Tropheryma whipplei
(
T. whipplei
) infection. The present study describes 3 cases of WD with clinical manifestations of cough, chest pain, headache, dyspnea, sputum, joint pain, abdominal pain, diarrhea and weight loss. Chest computed tomography (CT) showed signs of plaques, nodules and pleural thickening; and bronchoscopic alveolar lavage fluid metagenomic-sequencing indicated that it was
T. whipplei
. One patient was treated with meropenem as the starting regimen and two patients were treated with ceftriaxone as the starting regimen. Furthermore, two patients were provided with a maintenance regimen of cotrimoxazole and one was given a maintenance regimen of minocycline, which was combined with meropenem and ceftriaxone in order to improve their cough, chest pain, headache and dyspnea symptoms. To the best of our knowledge, there are few reports on WD of the respiratory system caused by
T. whipplei
, and differential diagnosis is the key to clinical diagnosis. When WD of the respiratory system is difficult to diagnose, metagenomic second-generation sequencing (mNGS) may be a better choice, which can achieve early diagnosis and early treatment. However, its clinical value is still limited; therefore, more research needs to be conducted in the future.