Background: Exhaled nitric oxide (FeNO) has been introduced in the diagnosis and control of asthma. Atopy related diseases are a common comorbidity in asthma, but in these cases the FeNO values and their relevance have not been clearly defined. In this study we compared the differences in FeNO levels in various atopic conditions. Methods: A prospective study was performed comparing online FeNO in six groups of patients (non-atopic control, asymptomatic atopic, non-active rhinitis, active rhinitis, asthma, asthma with rhinitis). Results: 90 children (15 per group) assisted in an outpatient hospital clinic were enrolled. FeNO levels (ppb) were: 7.9 (non-atopic control), 19 (asymptomatic atopic), 16.6 (non-active rhinitis), 26.3 (active rhinitis), 31 (asthma), and 35 (asthma and rhinitis). All groups presented higher levels of FeNO than the non-atopic control group (P < 0.001). Both asthma groups had higher levels than the rest of the groups (P < 0.05), except for the active rhinitis group. Dispersion of FeNO levels was wide in the study sample. No correlation was found between FeNO and FEV1. A weak correlation was seen with age V = 0.28) Conclusions: Atopy, rhinitis and its exacerbations can be confounders in the interpretation of FeNO levels in asthmatic children.