| Differential diagnosis | Investigation | Result |
| Bacterial LRTI | BAL microscopy and culture | Negative |
| Viral LRTI | BAL viral PCR and culture | Negative |
| Fungal LRTI | BAL cytology and culture | Negative |
| PCP | BAL cytology and PCR | Negative |
| Pulmonary TB | BAL acid-fast bacilli stain and culture; Mantoux test | Negative |
| Hypersensitivity pneumonitis | IgG and IgE precipitating antibodies to inhaled organic dusts | Negative |
| Connective tissue disorder | Autoimmune screen | Negative |
| Sarcoidosis | Serum ACE | Normal |
| Alveolar haemorrhage syndrome# | ANCA, Anti-GBM and BAL-haemosiderin laden macrophages | Negative |
| Histiocytosis | Bone marrow aspirate | Normal |
| Immunodeficiency | Igs and HIV tests | Normal |
| Congenital or acquired cardiac abnormality | Echocardiogram | Normal |
LRTI: lower respiratory tract infection; PCP: Pneuomocystis carinii pneumonia; TB: tuberculosis; BAL: bronchoalveolar lavage; Ig: immunoglobulin; ACE: angiotensin-converting enzyme; ANCA: anti-neutrophil cytoplasmic antigen; anti-GBM: anti-glomerular basement membrane antigen. #: Goodpasture’s disease or granulomatosis with polyangiitis (Wegener's).