Objectives: Limited data suggest complete mucosal healing in treated children with celiac disease (CD), but recent data from adult endoscopic biopsies have shown substantial numbers with persistent mucosal injury. We aimed to assess the rate of mucosal healing and indications for repeat small bowel (SB) biopsy in children with CD.Methods: We retrospectively reviewed records of children (ages 1–18 years) with CD who underwent a second SB biopsy. All of the children were seen at Mayo Clinic (Rochester, MN) from January 1997 through June 2013.Results: Forty children were identified (14 boys); average age at diagnosis was 8.5 years. Indications for second SB biopsy were abdominal pain (n = 20), diarrhea (n = 7), constipation (n = 5), non–celiac‐related concern (n = 2), follow‐up (n = 5), and persistent serology (n = 1). Average time between biopsies was 24 months (range 4–120 months). Histology on the second biopsy showed complete healing (n = 25), intraepithelial lymphocytes (n = 9), and persistent villous atrophy (n = 6). Of these, 3 patients had partial villous atrophy and 3 had with complete villous atrophy. Persistent villous atrophy was observed in 2 of 20 patients with abdominal pain and 1 of 7 with diarrhea. All of the patients with persistent constipation (n = 5) had complete resolution.Conclusions: Mucosal healing in children with CD may not be complete as previously assumed. Abdominal pain was the most common indication for repeating the SB biopsy. Persistence of abdominal pain, diarrhea, and constipation was poorly associated with persistence of mucosal injury.