We evaluated microfocal X- ray computed tomography (micro-CT) as a method to visualize lung architecture two- and three-dimensionally and to obtain morphometric data. Inflated porcine lungs were fixed by formaldehyde ventilation. Tissue samples (8 mm diameter, 10 mm height) were stained with osmium tetroxide and 400 projection images (1024 x 1024 pixel) were obtained. Continuous isometric micro-CT scans (voxel size 9 µm) were acquired to reconstruct two- and three-dimensional images. Tissue samples were sectioned (thickness 8 µm) for histologic analysis. Alveolar surface density and mean linear intercept were assessed by stereology-based morphometry in micro-CT scans and corresponding histologic sections. Furthermore, stereology-based morphometry was compared to morphometric semi-automated micro-CT analysis within the same micro-CT scan. Agreement of methods was assessed by regression- and Bland-Altman-analysis. Comparing histology with micro-CT, alveolar surface densities (35.4 ± 2.4 vs. 33.4 ± 1.9 / mm, p < 0.05) showed a correlation (r = 0.72; p = 0.018) with an agreement of 2 ± 1.6 /mm; the mean linear intercept (135.7 ± 14.5 vs. 135.8 ± 15 µm) correlated well (r = 0.97; p < 0.0001) with an agreement of -0.1 ± 3.4 µm. Semi-automated micro-CT analysis resulted in smaller alveolar surface densities (33.4 ± 1.9 vs. 30.5 ± 1 / mm; p < 0.01) with a correlation (r = 0.70; p = 0.023) and agreement of 2.9 ± 1.4 /mm. Non-destructive micro-CT scanning offers the advantage to visualize the spatial tissue architecture of small lung samples two- and three-dimensionally.