Background The results from experimental and clinical studies have shown that mechanical ventilation (MV) and/or hyperoxia may aggravate a pre-existing lung injury, or even cause lung injury in healthy lungs, despite the fact that it might be the only life-saving intervention available to a patient. The present study was designed to investigate the roles of MV and hyperoxia in the pathogenesis of lung injury. Methods Newborn New Zealand white rabbits were randomly assigned to an unventilated air control group or to one of the 2 × 3 × 3 ventilation strategies using a factorial design. The experimental groups were assigned different fractions of inspired oxygen (FiO2), peak inspiratory pressures (PIP), and respiratory times (RT). The lung wet-to-dry ratio (W/D), lung histopathology scores, and cells in the bronchoalveolar lavage fluid (BALF) were analyzed for each group. The apoptosis levels were studied by immunohistochemistry and a terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) assay. Results Different ventilation regimes induced alterations in microvascular permeability, differential histopathological grading, WBC and/or neutrophil and/or lymphocyte influx, and apoptosis levels; moreover, there were significant correlations and interaction effects between these indices. Conclusions Our data demonstrate that different ventilation regimes can induce lung injury and that the interaction effects of the FiO2, the PIP and the RT may play crucial roles in the pathogenesis of lung injury. Pediatr Pulmonol. 2012. 47:1103-1112. © 2012 Wiley Periodicals, Inc.