Invasive aspergillosis (IA) may occur as a serious complication of haematological malignancy. Delay in antifungal therapy can lead to an invasive disease resulting high mortality. Currently, there are no well-established biomarkers or laboratory tests to diagnose IA. Considering the impact of severity of infection, adequate blood biomarkers may prove to be valuable for timely disease diagnosis. During the past decade the connection between extracellular microRNA (miRNA) levels and several pathological processes, including different infections are increasingly recognized. miRNAs that circulate in blood are promising biomarkers for several infectious diseases. Therefore, we aimed to define deregulated miRNAs in haematology and oncology (HO) patients in order to identify diagnostic markers of IA. We performed an in-depth analysis of high-throughput small transcriptome sequencing data obtained from the whole blood samples of 26 HO patients with the indication of IA and 24 healthy controls. By integrating in silico bioinformatic analyses of small non-coding RNA data 57 miRNAs were identified exhibiting significant expression differences (P<0.05) in IA infected patients compared to the non-IA HO patients. Among these, we found 36 differentially expressed microRNAs (DEMs) irrespective of HO malignancy. Out of the top ranked DEMs, we found 14 miRNAs downregulated including hsa-miR-191-5p, hsa-miR-106b-5p, hsa-miR-16-2-3p, hsa-miR-185-5p, hsa-miR-26a-5p, hsa-miR-26b-5p, hsa-miR-106b-3p, hsa-miR-15a-5p, hsa-miR-20a-5p, hsa-miR-20b-5p, hsa-miR-106a-5p, hsa-miR-103a-5p, hsa-miR-93-5p and hsa-miR-17-5p whose expression levels were also quantified by qRT-PCR. MiRNA target prediction revealed that all IA-related miRNAs may cooperate in the regulation of key elements in biological pathways of tumorigenesis, cell cycle, immune response, cell differentiation and apoptosis.