The lungs are among general organs that can undergo irreversible damage from chronic alcohol consumption. Herein, we developed an animal model predisposed for edematous lung injury following chronic ingestion of alcohol in order to better understand the etiology of alcohol related disorders. Using animal modeling, alongside high throughput proteomic and microarray assays, we identified changes in lung protein and transcript in mice and rats, respectively, following chronic alcohol ingestion or a caloric control diet. Liquid chromatography-mass spectrometry (LC-MS/MS) identified several mitochondrial-related proteins in which the expression was up-regulated following long term alcohol ingestion in mice. Consistent with these observations, rat gene chip microarray analysis of alveolar cells obtained from animals maintained on a Lieber-DeCarli liquid alcohol diet confirmed significant changes in mitochondrial-related transcripts in the alcohol lung. Transmission electron microscopy (TEM) revealed significant changes in the mitochondrial architecture in alcohol mice, particularly following lipopolysacharide (LPS) exposure. Chronic alcohol ingestion was also shown to worsen mitochondrial respiration, mitochondrial membrane polarization, and NAD+/NADH ratios in alveolar type 2 cells. In summary, our studies show causal connection between chronic alcohol ingestion and mitochondrial dysfunction; albeit the specific role of each of the mitochondrial-related proteins and transcripts identified in our study requires additional study.