Introduction: Community-acquired pneumonia (CAP) and acute cardiogenic pulmonary oedema (ACPO) are common clinical conditions requiring hospital admission, but require different treatment. To assess whether exhaled breath analysis can distinguish between these, we measured exhaled breath condensate biomarkers and fractional exhaled nitric oxide (F E NO) in 14 patients with CAP and 12 patients with ACPO admitted acutely to hospital via the Emergency Department, comparing profiles with 15 control subjects. Methods: F E NO was measured using a NO Breath analyser and exhaled breath condensate (EBC) was collected for analysis of EBC biomarkers. EBC pH was measured with pH meter. The EBC biomarkers C-reactive protein (CRP), neopterin and 5N-terminal pro-brain natriuretic peptide (5NT-proBNP) were quantified using enzyme linked immunosorbent assays. Results: EBC 5NT-proBNP was raised in ACPO, while EBC CRP was raised in CAP. However, neopterin and pH showed no differences between groups. F E NO levels were significantly higher in CAP than in ACPO (p=0.03). Conclusions: This study demonstrates that exhaled breath analysis may be useful in assessing the acutely breathless patient, but that even this easy non-invasive technique is difficult for sick patients. More rapid measurements, application of novel biomarkers and combined assessment of several EBC biomarkers are likely to improve diagnostic differentiation in the future.