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Background and Objectives: Measurement of fractional exhaled nitric oxide (FeNO) concentration is currently used as a non-invasive biomarker to assess airway inflammation. Many factors can influence the FeNO level. However, there have been no reports concerning factors attributed to FeNO levels in different age groups of children, especially those with high FeNO values. Therefore, this study aimed to assess the influence of selected factors on nitric oxide concentration in exhaled air in children aged 8–9 attending class 3 of public primary schools in Krakow with high FeNO values ≥ 20 ppb. Materials and Methods: The population-based study covered all third-grade pupils attending primary schools in the city of Krakow. Five thousand, four hundred and sixty children participated in the first screening stage, conducted from October 2017 to January 2018. Then, 792 participants with an FeNO level ≥ 20 ppb were selected. Finally, those selected pupils were invited to participate in the second stage, diagnostic, in April 2018. Four hundred and fifty-four children completed the diagnostic stage of the study, and their data was included in the presented analysis. Results and Conclusions: Significantly higher FeNO levels were observed in children diagnosed with the following diseases: asthma, allergic rhinitis, atopic dermatitis, and allergy (p < 0.05). In addition, it was observed that a higher FeNO concentration characterised children taking antihistamines compared to children not taking those medications (p = 0.008). In multivariate models, we observed that regardless of sex, age, BMI value, home smoking, and whether they were taking medications, children who had allergic rhinitis, or atopic dermatitis, or allergies had significantly higher FeNO levels. The strongest relationship was noted with allergic diseases. The results of our study may be of importance to clinicians when interpreting FeNO results, for example, when making a therapeutic decision. [ABSTRACT FROM AUTHOR]