Background & Aim Background Growing evidence demonstrate that human mesenchymal stromal cells (MSCs) tailor their in vivo anti-inflammatory response depending on the specific inflammatory environment they encounter. Understanding the anti-inflammatory mechanisms of systemic or intratracheal administrated MSCs in a range of lung diseases, including cystic fibrosis (CF), is crucial to refine MSC-based cell therapies. The aim of this study was to determine the effects of the in vivo lung environment in CF patients on MSCs behavior. Methods, Results & Conclusion Methods Clinically utilized MSCs were exposed to bronchoalveolar lavage (BAL) fluids, a surrogate for the in vivo environment, obtained from patients with CF and healthy volunteers, or Gliotoxin. Following exposure, cells and conditioned medium were assessed for cytotoxicity, levels of immunomodulatory cytokines, and the presence of apoptotic markers. BAL-fluid samples were assessed for pro- and anti-inflammatory cytokines, osmolality, protease activity, gliotoxin concentrations, and double-stranded DNA content. Results Following five hours of BAL-fluid exposure, we found that a sub-population of BAL-fluid from CF-patients induced cellular death. Importantly, BAL-fluid from healthy volunteers did not induce any apparent MSCs death. Utilizing an RNAseq approach, we were able to identify the BCL-2 apoptotic pathway, which could be activated by Aspergillus fumigatus (Asp) a common infection seen in CF-patients, and found that only BAL-fluid from Asp+ CF-patients induced MSC death. Furthermore, we found that Gliotoxin, the major toxin produced by Asp, induced MSC death, an effect which was inhibited by addition of dithiothreitol (DTT). Finally, gliotoxin-exposed MSCs were shown to have less therapeutic effect compared to untreated MSCs in an acute lung injured mice model. Conclusions MSCs exposed to BAL-fluids from Aspergillus fumigatus infected CF-patients displayed an increased cellular death, and exposure to the major fungal toxin resulted in a decreased therapeutic capacity of MSCs in vivo.These results highlight the need to understand the effect of the in vivo inflammatory environment on systemic or locally administered MSCs.