The hydrogen (H2) breath test is a non-invasive investigation used to diagnose lactose intolerance (LI). Patients with LI may also expire increased amounts of methane (CH4) during a lactose test. The aim of this study is to evaluate the contribution of CH4 measurements. We tested 209 children (1–17 years old) with symptoms suggesting LI with lactose H2 and CH4 breath tests. The result was positive when the H2 excretion exceeded 20 parts per million (ppm) and the CH4 was 10 ppm above the baseline. A clinician, blinded for the results of the breath test, registered the symptoms. Of the patient population, 101/209 (48%) were negative for both H2 and CH4; 96/209 (46%) had a positive H2 breath test result; 31/96 (32%) were also positive for CH4; 12/209 (6%) patients were only positive for CH4. The majority of hydrogen producers showed symptoms, whereas this was only the case in half of the H2-negative CH4 producers. Almost all patients treated with a lactose-poor diet reported significant symptom improvement. These results indicate that CH4 measurements may possibly be of additional value for the diagnosis of LI, since 5.7% of patients were negative for H2 and positive for CH4, and half of them experienced symptoms during the test.