The quantitative histological analysis of airway innervation using tissue sections is challenging because of the sparse and patchy distribution of nerves. Here we demonstrate a method using a computational approach to measure airway nerve architecture that will allow for more complete nerve quantification and the measurement of structural peripheral neuroplasticity in lung development and disease. We demonstrate how our computer analysis outperforms manual scoring in quantifying three-dimensional nerve branchpoints and lengths. In murine lungs, we detected airway epithelial nerves that have not been previously identified because of their patchy distribution, and we quantified their three-dimensional morphology using our computer mapping approach. Furthermore, we show the utility of this approach in bronchoscopic forceps biopsies of human airways, as well as the esophagus, colon, and skin.