Pulmonary function testing has classically involved measurement of the lung's physical properties. Past research has defined normal lung mechanics, airflow, and gas exchange, allowing us to evaluate lung pathophysiology with respect to these entities. Recent studies, however, have shown that exhaled gas, instead of merely being physically measured, may contain valuable molecular clues to lung cell function. Recently, the common monoxides, nitric oxide (NO) and carbon monoxide (CO), have been explored as markers and mediators of lung biology. This article will explore the background information and recent clinical data on these emerging diagnostic modalities in adults.