A computerized system has been developed to monitor tidal volume, respiration rate, mouth pressure, and carbon dioxide during breath collection. This system was used to investigate variability in the production of breath biomarkers over an eight-hour period. Hyperventilation occurred when breath was collected from spontaneously breathing study subjects (n=8). Therefore, breath samples were collected from study subjects whose breathing were paced at a respiration rate of 10 breaths per minute and whose tidal volumes were gauged according to body mass. In this "paced breathing" group (n=16), end-tidal concentrations of isoprene and ethane correlated with end-tidal carbon dioxide levels (r_s=0.64, p=0.008 and r_s=0.50, p=0.05). Ethane also correlated with heart rate (r_s=0.52, p<0.05). There was an inverse correlation between transcutaneous pulse-oximetry and exhaled carbon monoxide (r_s=-0.64, p=0.008). Significant differences were identified between males (n=8) and females (n=8) in the concentrations of carbon monoxide (4 ppm in males vs. 3 ppm in females, p=0.01) and volatile sulfur containing compounds (134 ppb in males vs. 95 ppb in females, p=0.016). There was a peak in ethanol concentration directly following food consumption and a significant decrease in ethanol concentration two hours later (p=0.01, n=16). Sulfur containing molecules increased linearly throughout the study period (=7.4, p<0.003). Ventilation patterns strongly influence quantification of volatile analytes in exhaled breath and thus accordingly, the breathing pattern should be controlled to ensure representative analyses.