Exhaled nitric oxide (FENO) may provide a tool for identifying infants at risk of developing allergic disease in childhood. In infants there is no standardized collection technique; however, the easiest method is to measure FENO during tidal breathing. In this study we investigated various methodological issues for tidal breathing (TB) FENO in infants. These included the effect of ambient NO, oral or nasal breathing, sedation, and tidal expiratory flow. Furthermore, we compared TB FENO in 88 infants with and without wheeze. Ambient NO greater than 5 ppb significantly affected FENO. There was no significant difference between NO levels measured during either oral or nasal breathing; however, there was a significant difference between levels collected from infants before and after sedation (P < 0.001). Tidal breathing FENO decreased with increasing tidal flows (P < 0.001) and increased with age (P = 0.002). There was no significant difference in mixed expired NO between healthy and wheezy children, but children with doctor-diagnosed eczema had significantly raised levels (P = 0.014). There seem to be important methodological limitations for measuring FENO in infants during TB.