Objective: Few studies have investigated links between fraction exhaled nitric oxide (FeNO), the home and the school environment. FeNO is a biomarker of T helper 2 (Th2) airway inflammation. We investigated associations between FeNO and airway symptoms, allergies, household and classroom exposure among pupils in ten primary schools in Stockholm (N = 415). Methods: Information on health and household environment was obtained by a questionnaire. FeNO was measured at school. Particle mass (PM1, PM2.5, PM10), carbon dioxide (CO2), temperature, and relative air humidity (RH) were measured in the classrooms. Microbial DNA and 3-hydroxy fatty acids (3-OHs) from endotoxin in Gram-negative bacteria were analysed in vacuumed dust from floors and upper surfaces. Three-level linear mixed models were used to analyse associations. Results: In total, 9.7 % of the pupils had elevated FeNO (>20 ppb), 15.2 % doctor diagnosed asthma, 10.7 % current asthma, 17.8 % reported allergy and 9.6 % doctor diagnosed allergy. Reported allergy (p = 0.02), diagnosed allergy (p = 0.002), and current asthma (p = 0.007) were associated with elevated FeNO. Children living in single-family houses with basement had higher FeNO than those in self-owned apartments (p = 0.001). In the classrooms, PM10 (p = 0.008), RH (p = 0.004) and DNA copies from Gram-negative bacteria in vacuumed floor dust (p = 0.008) were associated with higher FeNO. C16 3-OH in floor dust (p = 0.046) and C10 (p = 0.02) and C11 3-OHs (p = 0.04) in upper surface dust were associated with higher FeNO. The association between Gram-negative bacteria at school and FeNO was stronger among girls. Children with parental asthma and allergy, and among those with dampness and mould at home and in single-family houses with basement. Conclusions: FeNO is associated with reported asthma and allergy. In the school environment, PM10 and exposure to some subpopulations of Gram-negative bacteria can increase FeNO. Sex, parental asthma or allergy, dampness at home and type of housing can modify associations between classroom exposure and FeNO.