Rationale: Despite numerous studies establishing male sex as an independent risk factor associated with the development of bronchopulmonary dysplasia (BPD), we lack a detailed understanding of the underlying mechanisms. Exposure to supplemental oxygen (hyperoxia) contributes to BPD pathophysiology. Lung endothelial cells (ECs) are particularly susceptible to hyperoxia exposure and display remarkable heterogeneity in their injury responses. The objective of this study was to identify key biological pathways modulated by gonadal hormones versus sex chromosomal complement in the distal lung capillary endothelium (aerocytes, aCap and general capillary cells, gCap) using a mouse model of BPD. Methods: To distinguish sex differences caused by gonadal hormones versus sex chromosome complement (XX versus XY), we used the four-core genotype (FCG) mice and exposed them to hyperoxia (95% FiO2, PND1-5: saccular stage of lung development) or room air. This model generates XX and XY mice that have either testis (with Sry, XXM or XYM) or ovaries (without Sry, XXF or XYF). Lungs from 3 mice/genotype/group were subjected to scRNA-Seq analysis. Additionally, we wanted to identify drugs/small molecules for individualized therapy using the transcriptome data from the NIH LINCs data base for drug discovery. Results: Transcriptional changes were evident in all endothelial cell subpopulations, with a remarkable impact on the distal capillary endothelium (Figure 1A-B). aCaps and gCaps from chromosomal males (XYM, XYF) and gonadal males (XYM, XXM) had a greater number of differentially expressed genes in response to hyperoxia compared to chromosomal females (XXF, XXM) and gonadal females (XXF, XYF), respectively (Figure 1C). Biological pathways unique to chromosomal males included cell surface receptor signaling pathway and regulation of phosphate metabolic process in aCap. While negative regulation of cell proliferation and cell communication biological pathways were unique to chromosomal males in gCap. Drug discovery analysis identified Enalaprilat, Trapidil, Deferiprone and Rifaximin as compounds that are likely to reverse the BPD phenotype in the distal endothelium in a sex-specific manner (Figure 1D). Conclusions: In summary, we show for the first time, that the transcriptional response in the distal lung capillary endothelium is modulated by the gonadal and chromosomal sex complement with males showing a greater response than females. We show that potential drug targets that can reverse the injury response in the endothelium is also modulated by sex as a variable. Validation of these novel findings will lead to a better understanding of the pathogenesis and offer targeted therapies to rescue abnormal vascular development in BPD.