An apparatus for analyzing nitric oxide levels in breath, comprising: a nasal sampling cannula; a breathing sensor to measure a breathing pattern parameter; a breath sampling system comprising a plurality of valves (V1-V7) to isolate sections of the breath gas sampling system; a pump downstream from at least two of the plurality of valves (V1-V7) that draws a plurality of breaths from a patient into the nasal sampling cannula and through the breath sampling system; a first processor containing executable instructions for analyzing breathing pattern parameters of the plurality of breaths; a second processor containing executable instructions for establishing in real-time, based on the analyzed breathing pattern parameters of the plurality of breaths, a breathing pattern parameter criteria that delineates between a physiologically representative breath and a physiologically non-representative breath; a third processor containing executable instructions for determining whether a breathing pattern parameter of a breath, exhaled after the plurality of breaths, meets the breathing pattern parameter criteria; a fourth processor containing executable instructions for, in response to a determination that a breathing pattern parameter of the breath meets the breathing pattern parameter criteria, delineating at least a first section of the breath, a second section of the breath, and a third section of the breath, wherein the first section of breath is exhaled before the second section of breath and the second section of breath is exhaled before the third section of breath; a fifth processor containing executable instructions for controlling the plurality of valves (V1-V7) to isolate the first section of breath, second section of breath, and third section of breath from each other; and an analyzer to analyze nitric oxide levels in at least one of the second section of the breath and the third section of the breath separately from the other. a nasal sampling cannula; a breathing sensor to measure a breathing pattern parameter; a breath sampling system comprising a plurality of valves (V1-V7) to isolate sections of the breath gas sampling system; a pump downstream from at least two of the plurality of valves (V1-V7) that draws a plurality of breaths from a patient into the nasal sampling cannula and through the breath sampling system; a first processor containing executable instructions for analyzing breathing pattern parameters of the plurality of breaths; a second processor containing executable instructions for establishing in real-time, based on the analyzed breathing pattern parameters of the plurality of breaths, a breathing pattern parameter criteria that delineates between a physiologically representative breath and a physiologically non-representative breath; a third processor containing executable instructions for determining whether a breathing pattern parameter of a breath, exhaled after the plurality of breaths, meets the breathing pattern parameter criteria; a fourth processor containing executable instructions for, in response to a determination that a breathing pattern parameter of the breath meets the breathing pattern parameter criteria, delineating at least a first section of the breath, a second section of the breath, and a third section of the breath, wherein the first section of breath is exhaled before the second section of breath and the second section of breath is exhaled before the third section of breath; a fifth processor containing executable instructions for controlling the plurality of valves (V1-V7) to isolate the first section of breath, second section of breath, and third section of breath from each other; and an analyzer to analyze nitric oxide levels in at least one of the second section of the breath and the third section of the breath separately from the other.