BACKGROUND Functional Gastrointestinal Disorders (FGIDs) are among the most common outpatient diagnoses in pediatric primary care and gastroenterology. There is limited data on the inpatient burden of childhood FGIDs in the U.S. The aim of this study was to evaluate the inpatient admission rate, length of stay, and associated costs related to FGIDs from 1997–2009. METHODS We analyzed the Kids’ Inpatient Sample Database (KID) for all subjects in which constipation (ICD-9 codes: 564.0–564.09), abdominal pain (ICD-9 codes: 789.0–789.09), irritable bowel syndrome (IBS) (ICD-9 code: 564.1), abdominal migraine (ICD-9 code:346.80 and 346.81)dyspepsia (ICD-9 code: 536.8) or fecal incontinence (ICD-codes: 787.6–787.63) was the primary discharge diagnosis from 1997–2009. The KID is the largest publicly available all-payer inpatient database in the U.S., containing data from 2–3 million pediatric hospital stays yearly. KEY RESULTS From 1997–2009, the number of discharges with a FGID primary diagnosis increased slightly from 6,348,537 to 6,393,803. The total mean cost per discharge increased significantly from $6115 to $18,058 despite the length of stay remaining relatively stable. Constipation and abdominal pain were the most common FGID discharge diagnoses. Abdominal pain and abdominal migraine discharges were most frequent in the 10–14 year age group. Constipation and fecal incontinence discharges were most frequent in the 5–9 year age group. IBS discharge was most common for the 15–17 year age group. CONCLUSIONS AND INFERENCES Hospitalizations and associated costs in childhood FGIDs have increased in number and cost in the U.S. from 1997–2009. Further studies to determine optimal methods to avoid unnecessary hospitalizations and potentially harmful diagnostic testing are indicated.