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Summary Background Disease severity in paediatric obesity is usually defined using the body-mass index (BMI). Although informative at the population level, its usefulness on an individual level has limitations. The use of a clinical staging system—Edmonton Obesity Staging System for Pediatrics (EOSS-P)—in identifying health risk has been proposed. This study aimed to examine the association between BMI class and EOSS-P stage. Methods This cross-sectional study was done in children with obesity aged 5–17 years who enrolled in the Canadian Pediatric Weight Management Registry (CANPWR) between May 31, 2013, and Oct 27, 2017, involving ten multidisciplinary paediatric weight management clinics in Canada. We classified participants into WHO BMI classes (class I as 2–3 SD scores, class II as >3 SD scores, and class III as >4 SD scores above the WHO growth standard median), and applied the EOSS-P staging system (stages 0, 1, and 2/3) based on the clinical assessment of coexisting metabolic, mechanical, mental health, and social milieu issues. Clinical information was extracted from medical records and reported using standardised case report forms. Associations of BMI class with EOSS-P stage were examined in children with complete data. Findings Of the 847 children with complete data, 546 (64%) had severe obesity based on BMI class (ie, class II or III) and 678 (80%) were EOSS-P stage 2/3. Stage 2/3 obesity-related health issues were common; mental health concerns were most common (520 [61%] of 847 children), followed by metabolic (349 [41%] of 847 children), social milieu (179 [21%] of 847 children), and mechanical (86 [10%] of 847 children) health issues. Mental health issues (eg, anxiety and attention-deficit hyperactivity disorder) were equally distributed across BMI classes, metabolic health issues were slightly more common in higher BMI classes, and mechanical (eg, musculoskeletal issues and sleep apnoea) and social milieu (eg, bullying and low household income) issues increased with increasing BMI class. Of children with class I obesity, 206 (76%) of 270 had overall EOSS-P stage 2/3, compared with 195 (85%) of 229 with class III obesity. Interpretation Physical and mental health issues were highly prevalent among children with obesity irrespective of BMI class. Participants with class III obesity carried the greatest health risk across subcategories of the EOSS-P. As BMI class increased, a concomitant increased disease burden in mechanical and social milieu issues was observed, whereas metabolic and mental health risks were high across BMI classes. Funding Canadian Institutes of Health Research, Ontario Ministry of Health, McMaster University, and McMaster Children's Hospital.