Although the general framework described in the joint American Thoracic Society/European Respiratory Society guidelines provides a useful and practical method for the interpretation of pulmonary function tests, several other measurements and functional indices, if understood correctly, may help in diagnosis and management of patients with respiratory diseases and in design of research protocols. This review provides information on the underlying physiology, interpretative caveats, and the evidence supporting the use of a number of these indices. Some of these measurements, such as the inspiratory fraction, inspiratory capacity/total lung capacity (IC/TLC), may offer additional prognostic information, while others, such as residual volume (RV)/TLC and forced expiratory volume in 3 s/forced vital capacity (FEV3/FVC), may help fill in the gaps between patient symptoms and more traditional indices of pulmonary function. Although most studies of non-traditional indices focus on airflow-limiting disorders, many can be fruitfully applied in other settings. Understanding the physiology that catalyzed these investigations will undoubtedly enrich the functional assessment armamentarium of the practicing clinician and researcher.