Background <p>The airways of the mammalian lung form a tree-like structure, starting from the trachea and branching out to the terminal bronchioles. This tree is composed of heterogeneous sub-structures or compartments, varying in morphological characteristics such as composition of airway epithelium, presence of cartilage plates, and number of smooth muscle cell layers or lumen diameter. These compartments may vary in their reaction to different pathological stimuli. Thus, when studying a particular lung disease, the compartments need to be investigated individually and not as part of a more global portmanteau compartment. In the symmetrically branching primate lungs, dividing the airway tree into generations is a common method to create morphologically homogeneous groups of airway segments. In common lab animals however, an asymmetrical branching pattern is present, where conventional branching-based grouping methods are unable to create meaningful results.</p> Methods <p>Therefore, a morphological clustering approach was tested in the current proof of principle study for its suitability of dividing airways into biologically meaningful sub-compartments. On this basis, an investigation of the distribution of pulmonary airway changes in a bronchopulmonary dysplasia rabbit model was conducted.</p> Results <p>The approach of clustering airway segments by morphology instead of branching pattern proved to be capable of creating meaningful airway compartments. This way, the distribution of differences that would not have been visible in a purely global comparison of morphological characteristics, could be identified between disease model and control group.</p> Conclusions <p>The employed clustering model is applicable to study the contribution of airway sub-compartments in pulmonary diseases. On this basis, targeted strategies for their mitigation may be developed.</p>