The diagnosis of invasive pulmonary aspergillosis (IPA) is still in challenge in clinical practice, particularly for those patients without an obvious neutropaenia. In this study, a well-validated qPCR method and Platelia galactomannan (GM) assay were compared for their diagnostic performance using paired samples of bronchoalveolar lavage (BAL) fluid and serum from predominantly non-neutropaenic patients. In the serum samples, qPCR showed a comparable performance with GM assay in terms of sensitivity and specificity. In the BAL samples, qPCR and GM assay both demonstrated a good sensitivity (90 vs. 90%); however, the specificity of qPCR was higher than that of GM assay (92.5 vs. 68.8%, P<0.001) in these samples. A better sensitivity was obtained with BAL compared with serum samples for both GM assay (90 vs. 50%) and qPCR (90 vs. 60%). In conclusion, in non-neutropaenic patients, BAL appears to provide improved sensitivity for both GM and qPCR assays. BAL qPCR offers a better diagnostic value for IPA compared with BAL GM assay, significantly increasing the specificity without affecting the sensitivity.