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This is the first study comparing three commercially available PCR assays for the detection of <i>Aspergillus</i> DNA from respiratory specimen of immunocompromised patients and the presence of <i>cyp51A</i> gene mutations. Bronchoalveolar lavages (BALs, <i>N</i> = 103) from patients with haematological/oncological underlying diseases were retrospectively investigated. The performance of three PCR assays, namely MycoGENIE^®<i>Aspergillus fumigatus</i> Real-Time PCR Kit (Adamtech), Fungiplex^®<i>Aspergillus</i> Azole-R IVD Real-Time PCR Kit (Bruker Daltonik GmbH) and AsperGenius^® (PathoNostics B.V.), were evaluated. All patients were categorised following current EORTC/MSG criteria, with exclusion of the PCR-results. From the 11 invasive pulmonary aspergillosis (IPA) probable samples, eight were detected with MycoGENIE^®, resulting in a sensitivity of 80% and a specificity of 73%. Furthermore, Fungiplex^® resulted in six positive BALs with a sensitivity of 60% and a specificity of 91% and AsperGenius^® in seven positive BAL samples, with a sensitivity of 64% and a specificity of 97%. No proven IPA was detected. One isolate showed phenotypically an azole-resistance, which was also detected in each of the tested PCR assays with the mutation in TR34. The here tested PCR assays were capable of reliably detecting <i>A. fumigatus</i> DNA, as well as differentiation of the common <i>cyp51A</i> gene mutations. However, evaluation on the AsperGenius^® assay revealed a low risk of false positive results.