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We previously showed that gut-directed hypnotherapy (HT) is highly effective in the treatment of children with functional abdominal pain (FAP) and irritable bowel syndrome (IBS). Aim of this follow-up study was to investigate the long-term effects of HT vs. standard medical treatment plus supportive therapy (SMT).All 52 participants of our previous randomized controlled trial (RCT) were invited to complete a standardized abdominal pain diary, on which pain frequency and pain intensity were scored. Furthermore, the Children's Somatization Inventory (CSI) and a general quality of life (QOL) questionnaire were filled out. Clinical remission was defined as >80% improvement in pain scores compared with baseline.All 27 HT patients and 22 out of 25 SMT patients participated in this study. Two patients of the SMT group were lost to follow-up and one refused to participate. After a mean duration of 4.8 years follow-up (3.4–6.7), HT was still highly superior to conventional therapy with 68 vs. 20% of the patients in remission after treatment (P=0.005). Pain intensity and pain frequency scores at follow-up were 2.8 and 2.3, respectively, in the HT group compared with 7.3 and 7.1 in the SMT group (P<0.01). Also, somatization scores were lower in the HT group (15.2 vs. 22.8;P=0.04). No differences were found in QOL, doctors' visits, and missed days of school or work between the two groups.The beneficial effects of gut-directed HT are long lasting in children with FAP or IBS with two thirds still in remission almost 5 years after treatment, making it a highly valuable therapeutic option.