The goal of this study is to evaluate the safety of Fecal Microbiota Transplantation (FMT) in children with Crohn's disease who are in remission. Safety will be the primary endpoint and Pediatric Crohn's Disease. Pediatric Crohn's Disease Activity Index (PCDAI) with other secondary endpoints including changes in gut microbial diversity will also be studied. All children will receive the equivalent of 50g of stools from a healthy donor into the jejunum through upper endoscopy. Also, 1-2 additional mucosal biopsies will be collected during patient's routine (standard of care) endoscopy. Subjects will have a total of 5 study visits within 24 weeks including phone call follow up on Day 7 after FMT.

The Investigators hypothesize that children with Crohn's disease who are in remission can receive a single endoscopic dose of FMT with no significant safety concerns.

All children will receive the equivalent of 50 g of stools from a healthy donor into the jejunum through upper endoscopy. Children will be seen at baseline, then 4 and 24 weeks after study drug administration begins. Stools will be collected and stored for gut microbial profiles during the study visit windows. In addition, a follow up telephone call will be performed 7 days after study drug is administered. If children undergo endoscopy as part of the standard of care, study staff will obtain 1-2 additional biopsies for evaluation of mucosal inflammation. This study will also capture any laboratory results if any of the subjects undergo laboratory testing as part of the standard of care. This study will define the effects of transplant on gut microbial profile using advanced molecular taxonomic approaches. Safety will be closely monitored by solicited (during defined telephone calls and study visits) and unsolicited adverse events (at all times). Safety will be the primary endpoint of this study. Secondary endpoints include Pediatric Crohn's Disease Activity Index (PCDAI), changes in gut microbial diversity - determined by gut microbial genomics and proteomics (16S ribosomal RNA, 16s rRNA), and outcome measures for mucosal inflammation and repair as reflected through laboratory testing such as the level for C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), inflammatory cytokines of the colonic mucosa as well as the stool calprotectin level.

Inclusion Criteria:

1. Age: 7-21 who have been diagnosed with Crohn's disease
2. Remission of disease defined as PCDAI <10
3. Needs upper GI endoscopy

Exclusion Criteria:

1. Unwilling to give informed consent/assent
2. Pregnancy and breast feeding in patient subjects of childbearing potential
3. Subjects with significant renal and liver dysfunction (creatinine > 2 mg/dl and direct bilirubin > 2 mg/dl)
4. Subjects with congenital or acquired immunodeficiency, or who are immunosuppressed due to conditions other than Crohn's disease (such as neoplastic disease or organ transplantation), have received or are receiving chemotherapy, or have been diagnosed with HIV.
5. Subjects with severe food allergies