The Coronavirus pandemic stresses the importance of eHealth techniques to monitor patients at home. Home monitoring of lung function in asthma and cystic fibrosis (CF) may help to detect deterioration of lung function at an early stage, but the reliability is unclear. We investigated whether lung function measurements at home were comparable to measurements during clinical visits. We analysed prospectively collected data of two one-year observational cohort studies in 117 children (36 with CF and 81 with asthma). All patients performed forced expiratory volume in one second (FEV) measurements with a monitor at home. Paired FEV measurements were included if the measurement on the home monitor was performed on the same day as the FEV measurement on the pneumotachometer during a two monthly clinical visit. Bland-Altman plots and linear mixed model analysis were used. The mean difference (home measurement was subtracted from clinical measurement) in FEV was 0.18 L in CF (95% confidence interval (CI) 0.08-0.27 L; < 0.001) and 0.12 L in asthma (95%CI 0.05-0.19 L; < 0.001). FEV measurements at home were significantly lower than clinically obtained FEV measurements, which has implications for the application of this technique in the daily clinical situation.