Carbohydrate malabsorption and subsequent gastrointestinal symptoms are a common clinical problem in pediatrics. Hydrogen (H2) and methane (CH4) breath tests are a cheap and non-invasive procedure for diagnosing fructose and lactose malabsorption (FM/LM) but test accuracy and reliability as well as the impact of non-hydrogen producers (NHP) is unclear. CH4 breath tests (MBT), blood sugar tests (BST) and clinical symptoms were compared with H2 breath tests (HBT) for FM/LM. 187/82 tests were performed in children (2 to 18 years) with unclear chronic/recurrent abdominal pain and suspected FM/LM. In FM and LM, we found a significant correlation between HBT and MBT/BST. In LM, MBT differentiated most of the patients correctly and BST might be used as an exclusion test. However, additional MBT and BST had no diagnostic advantage in FM. NHP still remain a group of patients, which cannot be identified using the recommended CH4 cut-off values in FM or LM. Reported symptoms during breath tests are not a reliable method to diagnose FM/LM. Overall a combined test approach might help in diagnosing children with suspected carbohydrate malabsorption.