Objective: The aim was to assess the relationship between morning fractional exhaled NO (FeNO) and nocturnal oxygen desaturation in children. Design: prospective study. Setting: The study was conducted from January 2012 to January 2018, in the division of pediatric at tertiary-care hospital.Patients: Of the total of 112 children initially enrolled, 109 (case children; 65.1% males; age 7.0± 3.1 years) met the criteria of the oxygen desaturation index (≥ 1 desaturations measured by pulse oximetry). An additional 63 healthy children (controls, 60.3% males; age 7.9±2.9 years) were enrolled as external controls. Children underwent pulse oximetry (172 subjects), were assessed for FeNO and for inhalant allergens (skin prick test). Comorbidities were allergy and obesity. Methods: Nocturnal at-home oximetry and morning FeNO levels.Results: FeNO levels was comparable between case children without comorbidities and controls (p = 0.346). FeNO levels were much higher in case children with atopy compared to controls (p=0.0011) and in those with atopy and overweight compared to controls (p<0.0001) while FeNO levels increased in case children overweight compared to controls (p=0.0311). Conclusion:Atopy was the main determinant of elevated FeNO levels in children with nocturnal oxygen desaturation. A novel finding is that the FeNO levels were significantly increased in obese children as compared to controls. Further studies are needed to confirm our findings and to compare FeNO levels in obese children with or without recurrent desaturation events during sleep.