Clinical disease activity and endoscopic severity correlate poorly in children newly diagnosed with Crohn's disease. 
Treatment goals in Crohn's disease (CD) have evolved to target mucosal healing.  There is now a drive to determine if noninvasive measures can adequately identify the attainment and persistence of this goal.  Currently, data describing the relationship between clinical indices and endoscopic appearance in pediatric CD are sparse.  Our aim was to compare endoscopic severity with the weighted Pediatric Crohn's Disease Activity Index (wPCDAI) in children with newly diagnosed CD.  All children aged ≤17 years newly diagnosed with CD enrolled in an inception cohort at sites of the Canadian Children Inflammatory Bowel Disease Network were eligible.  Clinical disease activity at presentation was evaluated by the wPCDAI and conventional biochemical parameters.  Severity of disease at ileocolonoscopy was assessed by the simple endoscopic score for CD (SES-CD), with segmental subscores noted.  We evaluated the association of SES-CD and disease activity markers using the Pearson test of correlation, the Spearman rank coefficient, and linear regression models.  Two hundred eighty patients from 11 centers were included in the analysis.  The median wPCDAI score was 60 (interquartile range, 40-80; 53% severe).  Median SES-CD was 16 (interquartile range 10-22; 51% severe).  The wPCDAI correlated weakly with SES-CD (r = .39, P < .001).  Examination of the individual components that contribute to the wPCDAI demonstrated weak correlation with the SES-CD for all items apart from stooling (moderate correlation, r = .50, P < .001).  Routine blood tests did not correlate well with the SES-CD.  In regression models, variation in clinical symptoms accounted for most of the variation in both the wPCDAI and SES-CD, with no additional benefit from routine blood tests.  In children with newly diagnosed CD, wPCDAI correlates poorly with endoscopic disease activity.  As treatment paradigms evolve to target mucosal healing, clinical markers should not be used in isolation to determine disease activity.