The joint American Thoracic Socity (ATS) and European Respiratory Society (ERS) guidelines recommend design-based stereology for quantitative morphology of lung structures in health and disease (DOI: 10.1164/rccm.200809-1522ST). Design-based stereology is founded on stochatic geometry and rigorous sampling protocols to obtain a set of images which is representative for the whole organ so that the generated data are accurate (unbiased) and sufficiently precise. Regarding quantitative light and electron microscopic analyses lungs were fixed by airway instillation fixation using 1.5 % glutaraldehyde, 1.5% paraformaldehyde in 0.15M HEPES buffer at a hydrostatic pressure of 25 cmH2O. Afterwards lungs were subjected to a systematic uniform random sampling for light and transmission electron microscopy based on established protocols (DOI: 10.1016/j.aanat.2013.04.011). Regarding light microscopy, 3 to 4 tissue samples were taken randomly per lung, embedded in plastic (Technovit 8100), sectioned (thickness of 1.5 µm) and stained with toluidine blue. Whole slides were scanned (AxioScanZ.1) and subjected to a systematic uniform area sampling process using newCAST-stereology software (Visiopharm, Hoersholm, Denmark) to image 10% of the section. Depending on the size of the section the goal was to obtain at least 60 (in general >100) randomized light microscopic images per lung for quantitative assessment. Moreover, 6 tissue blocks were randomly taken for transmission electron microscopy, embedded in epoy resin (Epon) and sectioned with a thickness of 80nm. Using an electron microscope (FEI Morgagni transmission electron microscope, Eindhoven, The Netherlands), a systematic uniform area samplinbg was performed and at least 100 micrographs were randomly taken per lung. The dataset in this publication contains the representative light and transmission electron microscopic images of lungs from six different experimental groups (male Fisher 344 rats, aged 11-13 weeks). Healthy rat lung were either not mechanically ventilated (H/ No ventil) or mechanically ventilated with positive end-exspiratory pressure (PEEP) = 1 cmH2O (group H/PEEP1) or PEEP = 5 cmH2O (group H/PEEP5). In addition, lungs suffering from occult lung injury due to bleomycin instillation were also either not mechanically ventilated (B/No ventil) or ventiled with PEEP = 1 cmH2O (B/PEEP1) or PEEP = 5 cmH2O (B/PEEP5). The respiratory rate was 90/min and the tidal volume was 10ml/ kg bodyweight.