Breath analysis is a powerful non-invasive technique for the diagnosis and monitoring of respiratory diseases, including asthma and chronic obstructive pulmonary disease (COPD). Exhaled nitric oxide (NO) and carbon monoxide (CO) are markers of airway inflammation and can indicate the extent of respiratory diseases. We have developed a compact fast response quantum cascade laser system for analysis of multiple gases by tunable infrared absorption spectroscopy. The ARI breath analysis instrument has been deployed in a study of exhaled breath from patients with asthma or COPD. A total of 173 subjects participated, including both adult and pediatric patients. Patients in asthma or COPD exacerbations were evaluated twice-during the exacerbation and at a follow-up visit-to compare variations in breath biomarkers during these events. The change in exhaled NO levels between exacerbation and 'well' visits is consistent with spirometry data collected. Respiratory models are important for understanding the exchange dynamics of nitric oxide and other species in the lungs and airways. At each patient's visit, tests were conducted at four expiratory flow rates. We have applied a trumpet model with axial diffusion to the multi-flow exhaled nitric oxide data, obtaining NO alveolar concentrations and airway fluxes. We found higher airway fluxes for those with more severe asthma and during exacerbation events. The alveolar concentrations from the model were higher in adults with asthma and COPD, but this trend was less clear among the pediatric subjects.