Background Mucosal healing is now preferred over clinical remission as a target endpoint in the treatment of Ulcerative Colitis (UC) as it has been demonstrated to reduce hospitalisation and corticosteroid use, to reduce the risk of colectomy and to reduce the risk of colorectal cancer. In routine practice, the activity and severity of UC is based on combined clinical and endoscopic assessment in addition to histology. However, it is not clear whether the currently available histologic indices can help predict disease course and treatments. Mucosal atrophy (MA) describes a state of extensive mucosal architectural damage, causing irregularities in the morphology and distribution of the intestinal glands of the mucosa. The aim of this study was to investigate the prevalence of MA in a paediatric cohort of newly diagnosed patients with UC and evaluate the relationship between the presence of MA, disease activity and treatments. Methods Children Results 176 patients with UC were included of which 21 (12%) had MA on biopsy at diagnosis (mean age 11.9 years, 51% female). Those with MA had higher PUCAI scores at three month (p=0.04), six month (p=0.01) and two year (p=0.01) follow up. MA patients had significantly higher rates of progression to immunomodulators (58% vs 44%) and biologics (25% vs 11%), were more likely to have a clinical relapse (p=0.04) and had shorter times to first relapse post diagnosis (p=0.01). Conclusion Children with UC and mucosal atrophy demonstrate a more severe disease course with higher disease activity scores and rates of relapse, which results in increased rates of progression to more intensive therapies. Further research into the mechanisms underlying the more severe disease course of mucosal atrophy patients is warranted.