Spatial heterogeneity of lung aeration and strain (change volume/resting volume) occurs at microscopic levels and contributes to lung injury. Yet, it is mostly assessed with histograms or large regions-of-interest. Spatial heterogeneity could also influence regional gene expression. We used positron emission tomography (PET)/computed tomography (CT) to assess the contribution of different length-scales to mechanical heterogeneity and to direct lung injury biological pathway identification. Sheep exposed to mild (n = 5, supine and n=3, prone) and moderate (n=6, supine) systemic endotoxemia were protectively ventilated. At baseline, 6 hours and 20 hours length-scale analysis was applied to aeration in CT (mild groups) and PET transmission (moderate group) scans; and voxel-level strain derived from image registration of end-inspiratory and end-expiratory CTs (mild). 2-deoxy-2-[(18)F]fluoro-d-glucose (18F-FDG)-PET kinetics parameters in ventral and dorsal regions were correlated with tissue microarray gene expression (moderate). While aeration and strain heterogeneity were highest at 5-10 mm length-scales, larger length-scales contained a higher fraction of strain than aeration heterogeneity. Contributions of length-scales >5-10 mm to aeration and strain heterogeneity increased as lung injury progressed (p < 0.001) and were higher in supine than prone animals. Genes expressed with regional correlation to 18F-FDG-PET kinetics (|r|=0.81 [0.78-0.85]) yielded pathways associated with immune system activation and fluid clearance. Normal spatial heterogeneity of aeration and strain suggest larger anatomical and functional determinants of lung strain than aeration heterogeneity. Lung injury and supine position increase the contribution of larger length-scales. 18F-FDG-PET-based categorization of gene expression results in known and novel biological pathways relevant to lung injury. Copyright 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.