Objectives: The relevance of methane measurement in breath tests for the detection of carbohydrate malabsorption in children is controversial. The need for correction for poor sample collection is disputed. We evaluated the relevance of methane/CO2 measurements for the diagnosis of paediatric carbohydrate malabsorption. Methods: A total of 132 breath tests (fructose: n = 54; lactose: n = 78) were performed in 91 children/adolescents with functional abdominal complaints. Breath samples were collected and analysed for hydrogen, methane, and CO2. Malabsorption was defined by a net increase over baseline of ≥20 parts per million (ppm) for hydrogen, ≥5 to ≥12 ppm for methane, and ≥10 to ≥15 ppm for hydrogen-plus-methane. The diagnosis was made before and after the use of a CO2-based correction factor (5.5% as the numerator). Hydrogen-based test results were compared with results obtained with other cut-off values. Results: Fifty-eight positive tests were obtained by hydrogen measurement (without CO2 correction). The addition of methane measurements did not significantly influence the test results (P > 0.05). Only under the use of extraordinary cut-offs (combined hydrogen-plus-methane smaller than ≥18 ppm) did the rate of malabsorbers increase significantly (P < 0.05). After CO2 correction, hydrogen ≥20 ppm was detected in 4 additional patients, but 1 patient lost the hydrogen-based diagnosis of malabsorption (Cohen kappa = 0.92). Conclusions: Methane measurement did not significantly affect the detection rate of carbohydrate malabsorbers in children/adolescents with functional abdominal complaints when established cut-offs are used. The use of CO2 correction altered the diagnosis of malabsorption in a minority of patients but did not significantly alter overall test results.