BACKGROUND: Little is known about the long-term outcomes of bariatric surgery for severe adolescent obesity, raising questions about the durability of early responses to surgery. We aimed to analyse long-term (>5 years) outcomes of Roux-en-Y gastric bypass in a cohort of young adults who had undergone the operation during adolescence, in the Follow-up of Adolescent Bariatric Surgery at 5 Plus Years (FABS-5+) extension study. METHODS: A cohort of young people aged 13-21 years underwent Roux-en-Y gastric bypass for clinically severe obesity at a paediatric academic medical centre in the USA. We did a prospective follow-up analysis of these patients' outcomes 5-12 years after surgery. Outcomes assessed included BMI, comorbidities, micronutrient status, safety, and other risks. The FABS study is registered with ClinicalTrials.gov, number NCT00776776. FINDINGS: Between May, 2001, and February, 2007, 74 young people underwent Roux-en-Y gastric bypass in the FABS study. Of these, 58 individuals were eligible for the FABS-5+ study, could be located, and agreed to follow-up assessment. At baseline, the mean age of the cohort was 17·1 years (SD 1·7) and mean BMI was 58·5 kg/m2 (10·5). At mean follow-up of 8·0 years (SD 1·6; range 5·4-12·5), the mean age of the cohort was 25·1 years (2·4) and mean BMI was 41·7 kg/m2 (12·0; mean change in BMI -29·2% [13·7]). From baseline to long-term follow-up, significant declines were recorded in the prevalence of elevated blood pressure (27/57 [47%] vs 9/55 [16%]; p=0·001), dyslipidaemia (48/56 [86%] vs 21/55 [38%]; p<0·0001), and type 2 diabetes (9/56 [16%] vs 1/55 [2%]; p=0·03). At follow-up, 25 (46%) of 58 patients had mild anaemia (ie, not requiring intervention), 22 (45%) had hyperparathyroidism, and eight (16%) had low amounts of vitamin B12 (ie, below the normal cutpoint). INTERPRETATION: Roux-en-Y gastric bypass surgery resulted in substantial and durable bodyweight reduction and cardiometabolic benefits for young adults. Long-term health maintenance after Roux-en-Y gastric bypass should focus on adherence to dietary supplements and screening and management of micronutrient deficiencies. FUNDING: Ethicon Endosurgery, National Center for Advancing Translational Sciences (US National Institutes of Health). Copyright © 2017 Elsevier Ltd. All rights reserved.