Background & Aims: Although, the currently approved optimal treatment goal in Crohn’s disease (CD) is mucosal healing (MH), transmural healing (TH) is emerging as a new goal, facilitated by the development of magnetic resonance enterography (MRE). We aimed to investigate factors associated with TH in pediatric CD patients under maintenance treatment with biologics. Methods: This retrospective study was conducted at the Department of Pediatrics, Samsung Medical Center. Pediatric CD patients in whom ileocolonoscopies and MRE were performed simultaneously before starting treatment with biologics and at 1-year ± 2-years follow-up were included. MH was defined as a Simple Endoscopic Score for Crohn’s disease (SES-CD) 3. Complete ( Partial) TH was defined as wall thickness ≤ 3 mm ( ≤ 4 mm) with the absence of ulcers, edema, contrast hyperenhancement, fat creeping, Comb’s sign, and complications on all ileocolonic segments evaluated by MRE. MaRIA cut-off points for predicting MH and TH were also derived. Results: A total 72 patients were included in this study. At 1-year, MH, complete TH, and partial TH were achieved in 59.7% (43/72), 5.6% (4/72), and 16.7% (12/72) of the subjects, respectively. At 2-years, MH, complete TH, and partial TH were achieved in 66.7% (16/24), 13% (3/24), and 4.2% (1/24), respectively. All 20 patients who achieved complete or partial TH at 1- or 2-years also achieved MH. Moreover, all 7 patients who achieved complete TH demonstrated a SES-CD score of 0. SES-CD and MaRIA scores were each significantly lower in those who achieved complete/partial TH compared to those who did not (SES-CD: median 1 vs. 0, P=0.009; MaRIA: 42.5 vs. 31.5, P0.001). The optimal MaRIA cut-off point for predicting MH, complete TH, and complete/partial TH was 52.1 (AUC=0.772, 95% CI=0.668-0.875, sensitivity 94.9%, specificity 52.8%, P0.001), 35.3 (AUC=0.967, 95% CI=0.932-1.000, sensitivity 100%, specificity 87.5%, P0.001), and 38.7 (AUC=0.907, 95% CI=0.86-0.955, sensitivity 90.5%, specificity 83.6%, P0.001), respectively. Conclusions: Approximately one-third of patients with MH are capable of achieving at least partial TH, and among them only one-third are capable of achieving complete TH. Although, TH is a more stringent goal compared to MH, efforts to achieve TH may alter the natural course of CD in the era of treat-to-target.