Pulmonary Langerhans’ cell histiocytosis (PLCH) and lymphangioleiomyomatosis (LAM) are two rare cystic lung diseases of unknown aetiology and different pathogenesis. Although the diagnosis can be strongly suspected on the basis of the medical history and clinical and radiological features, at times a pathological confirmation of the diagnosis is necessary. Surgical lung biopsy is considered the gold standard in the diagnosis of both LAM and PLCH. However, bronchoalveolar lavage (BAL) and transbronchial lung biopsy (TBB) are less invasive procedures that can be useful in diagnosis. BAL has a high specificity but low sensitivity for PLCH, and in an appropriate clinical context it can be used to establish the diagnosis. However, even if a high percentage of pigment-laden macrophages are found in the BAL fluid of patients with LAM, no BAL findings are considered suggestive for the disease. TBB shows a low diagnostic yield (10–40%) in PLCH because of the small amount of tissue obtained and the patchy nature of the disease, although it may be of more use in LAM.