Background:A large body of evidence has now accumulated describing the advantages of multiple breath washout tests over conventional spirometry in cystic fibrosis (CF). Although the majority of studies have used exogenous sulphur hexafluoride (SF6) as the tracer gas this has also led to an increased interest in nitrogen washout tests, despite the differences between these methods. The impact of body nitrogen excreted across the alveoli has previously been ignored.Methods:A two-compartment lung model was developed that included ventilation heterogeneity and dead space (DS) effects, but also incorporated experimental data on nitrogen excretion. The model was used to assess the impact of nitrogen excretion on washout progress and accuracy of functional residual capacity (FRC) and lung clearance index (LCI) measurements.Results:Excreted nitrogen had a small effect on accuracy of FRC (1.8%) in the healthy adult model. The error in LCI calculated with true FRC was greater (6.3%), and excreted nitrogen contributed 21% of the total nitrogen concentration at the end of the washout. Increasing DS and ventilation heterogeneity both caused further increase in measurement error. LCI was increased by 6-13% in a CF child model, and excreted nitrogen increased the end of washout nitrogen concentration by 24-49%.Conclusions:Excreted nitrogen appears to have complex but clinically significant effects on washout progress, particularly in the presence of abnormal gas mixing. This may explain much of the previously described differences in washout outcomes between SF6 and nitrogen. © 2013 Nielsen et al.