Study design. BAL fluid from pediatric HCT candidates underwent RNA sequencing (RNAseq), and results were correlated with patient outcomes. Bronchoscopy with BAL was performed prior to allogeneic HCT in children. Samples underwent metatranscriptomic RNAseq to identify parallel microbiome and gene expression signatures associated with post-HCT clinical outcomes. These data may inform future strategies to optimize pre-HCT pulmonary health to maximize post-HCT survival in children.