To evaluate red flags as an instrument to distinguish other medical conditions from Functional Gastrointestinal Disorders (FGID) in children with long-term abdominal pain. In a retrospective follow-up, data were collected from 317 children who were referred for medical assessment due to long-term abdominal pain between the years 2011 and 2012 at three Swedish paediatric open clinic units in Sweden. Throughout the review of medical records, any documented red flags at the primary consultation and finally set diagnosis after 1 year were noted for all cases. A non-FGID disease was diagnosed in 32 cases (10.1%). The sensitivity of red flags to predict inflammatory bowel disease (IBD) was 100% and the specificity 64.1%. The sensitivity of red flags to predict celiac disease was 45.5% and the specificity 63.7%. The sensitivity of red flags to predict any non-FGID disease was 59.4%, and the specificity was 65.6%. The use of red flags is a sensitive instrument to identify patients with IBD but less applicable when identifying celiac disease and other organic diseases. Specificity is generally low and future biomarkers for assessing children with long-term abdominal pain is needed.