Introduction: miRNAs are key regulators of various physiological and pathophysiological processes and their altered expression levels have been associated to many diseases. Increasing number of evidences have demonstrated that specific miRNAs can serve as novel biomarkers for clinical diagnosis of diseases. Invasive aspergillosis is life-threatening systemic fungal infection. Regrettably, the standard diagnostic methods for this condition take days to produce a reliable result. Objectives: The aim of this study was to probe the expression profiles of 15 selected miRNAs in patients, with fevered neutropenia. We hypothesized that invasive aspergillosis could change the miRNA profiles in the blood. Our goal was to make a rapid test supporting diagnosis of invasive mycoses. Methods: We obtained whole blood samples from 16 patients suffering neutropenic fever and from 5 healthy volunteers without neutropenic fever. Total RNA was isolated from the whole blood and were reverse transcribed to cDNA. TaqMan® quantitative real-time PCR (miRNA assay) was used for detecting miRNA expression profiles. Relative mRNA expressions were calculated with the ΔΔCt method. Results: 7 out of the 19 miRNAs showed significant upregulation in the expression levels at p<0.05. Conclusion: The miRNAs with significantly different expression between the test group and the control can be used as informative biomarkers to assess and monitor the body’s physio-pathological status in invasive aspergillosis.