Acute lung injury (ALI) is a common and frequently devastating illness characterized by acute hypoxemic respiratory failure, profound inflammation, and flooding of the alveoli. Despite recent advances in ALI care, the morbidity and mortality of ALI continues to be unacceptably high. ALI-inciting events (e.g., sepsis, trauma, aspiration, pneumonia) are quite common, yet only a fraction of patients develop the syndrome. This heterogeneity of patients presenting with ALI has sparked interest in identifying the role of genetic factors that contribute to ALI susceptibility and prognosis. Recent advances in high-throughput sequencing and expression technologies now provide the tools to perform large-scale genomic analyses in complex disorders such as ALI; gene expression profiling and pathway analysis provide further insight into previously described molecular pathways involved in the syndrome. In this article, we describe the use of genomewide association studies, ortholog in silico techniques, utility of consomic rat methods, and candidate gene approaches using expression profiling and pathway analyses. These methods have confirmed suspected ALI candidate genes (e.g., IL-6 and MIF), but more impressively have identified novel genes (e.g., GADD45alpha and PBEF) not previously suspected in ALI. The analysis of the molecular pathways (e.g., the cytoskeleton in vascular barrier regulation) has identified additional genes contributing to the development and severity of ALI (e.g., MLCK), thereby providing therapeutic targets in this devastating illness.