The extrapolation to humans of studies of infectious or toxic agents injurious to the respiratory system using animal models assumes comparability in the structure and function of animal models and humans. Measurement of conducting airways and parenchyma yields quantitative data for parameters like volume, surface area, length, cell number and cell size. Over the past few decades, there has been an evolution of rigorous uniform sampling designs of stereology that ensure unbiased estimates of number, length, surface area, and volume. This approach has been termed 'design-based' stereology because of the reliance on sampling design rather than geometric model-based stereology that makes assumptions. The aim of this paper is to define new design-based stereological approaches for the direct estimation of anatomical structures and epithelial, interstitial and endothelial cells of specific regions of the lung independent of the sampling, size, orientation and reference traps. An example is provided using wildtype and transgenic mice expressing transforming growth factor-alpha to show the importance of the reference trap in stereologic estimates of postnatal lung growth.