Copyright © 2018 by the American Thoracic Society. The airway surface functional microanatomy, including the ciliated airway epithelium and overlying mucus layer, is a critical component of the mucociliary escalator apparatus, an innate immune defense that helps to maintain a clean environment in the respiratory tract. Many genetic and acquired respiratory diseases have underlying pathophysiological mechanisms in which constituents of the airway surface functional microanatomy are defective. For example, in cystic fibrosis, mutations in the cystic fibrosis transmembrane conductance regulator gene, which normally produces a secretory anion channel protein, result in defective anion secretion and consequent dehydrated and acidic mucosal layer overlying the airway epithelium. This thick, viscous mucus results in depressed ciliary beating and delayed mucociliary transport, trapping bacteria and other pathogens, compromising host defenses and ultimately propagating disease progression. Thus, developing tools capable of studying the airway surface microanatomy has been critical to better understanding key pathophysiological mechanisms, and may become useful tools to monitor treatment outcomes. Here, we discuss functional imaging tools to study the airway surface functional microanatomy, and how their application has contributed to an improved understanding of airway disease pathophysiology.