Rare diseases that primarily involve the gastrointestinal system. Each links to its full hub — overview, specialists, clinical trials, medications and community.
How this grouping is built. These conditions are grouped by a clinical keyword match on the disease name — the same conservative classifier Tomeko uses to pick each hub’s system motif. It is a Tomeko working grouping, not an official Orphanet organ classification, and some conditions affect more than one system. Every condition is itself catalogued from NIH GARD (Genetic and Rare Diseases Information Center) and Orphanet (orpha.net), and each hub cites its own sources. Sorted A→Z by name · 178 conditions · last built 2026-08-30.
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A6
B5
C31
- Childhood Malignant Small Intestinal Neoplasm
- Childhood Pancreatic Acinar Cell Carcinoma
- Childhood Pancreatic Acinar Cell Cystadenocarcinoma
- Childhood Small Intestinal Leiomyosarcoma
- Cholestasis Of Pregnancy
- Cholestasis, Intrahepatic, Of Pregnancy, 1
- Cholestasis, Intrahepatic, Of Pregnancy, 3
- Cholestasis, Progressive Familial Intrahepatic, 10
- Cholestasis, Progressive Familial Intrahepatic, 11
- Cholestasis, Progressive Familial Intrahepatic, 12
- Cholestasis, Progressive Familial Intrahepatic, 13
- Cholestasis, Progressive Familial Intrahepatic, 4
- Cholestasis, Progressive Familial Intrahepatic, 5
- Cholestasis, Progressive Familial Intrahepatic, 6
- Cholestasis, Progressive Familial Intrahepatic, 7, With Or Without Hearing Loss
- Cholestasis, Progressive Familial Intrahepatic, 8
- Cholestasis, Progressive Familial Intrahepatic, 9
- Cholestasis-Edema Syndrome, Norwegian Type
- Cholestasis-Pigmentary Retinopathy-Cleft Palate Syndrome
- Chronic Atrial And Intestinal Dysrhythmia
- Chronic Enteropathy Associated With SLCO2A1 Gene
- Chronic Intestinal Failure
- Chronic Intestinal Pseudoobstruction
- Cleft Lip/palate-Intestinal Malrotation-Cardiopathy Syndrome
- Combined Pancreatic Lipase-Colipase Deficiency
- Complement Hyperactivation-Angiopathic Thrombosis-Protein-Losing Enteropathy Syndrome
- Congenital Bile Acid Synthesis Defect 2
- Congenital Diarrhea 7 With Exudative Enteropathy
- Congenital Pancreatic Cyst
- Congenital Short Bowel Syndrome
- Congenital Short Bowel Syndrome, Autosomal Recessive
D1
E3
F4
G6
H5
I22
- IL10-Related Early-Onset Inflammatory Bowel Disease
- IL21-Related Infantile Inflammatory Bowel Disease
- Immune Dysregulation-Inflammatory Bowel Disease-Arthritis-Recurrent Infections-Lymphopenia Syndrome
- Infant Botulism
- Inflammatory Bowel Disease 1
- Inflammatory Bowel Disease 25
- Inflammatory Bowel Disease 28
- Inflammatory Skin And Bowel Disease, Neonatal, 1
- Inflammatory Skin And Bowel Disease, Neonatal, 2
- Intellectual Developmental Disorder With Gastrointestinal Difficulties And High Pain Threshold
- Intestinal Atresia
- Intestinal Botulism
- Intestinal Lymphangiectasia
- Intestinal Malrotation
- Intestinal Neuroendocrine Neoplasm
- Intestinal Obstruction In The Newborn Due To Guanylate Cyclase 2C Deficiency
- Intestinal Polyposis Syndrome
- Intestinal Pseudo-Obstruction
- Intestinal Pseudoobstruction, Neuronal, Chronic Idiopathic, X-Linked
- Intestinal Schistosomiasis
- Intestinal Tuberculosis
- Intestinal Variant Cervical Mucinous Adenocarcinoma
J1
K1
M11
- Malignant Atrophic Papulosis
- Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome 1
- Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome 2
- Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome 3
- Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome 4
- Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome 5
- Melanoma-Pancreatic Cancer Syndrome
- Mesenchymal Tumor Of Small Intestine
- Multiple Gastrointestinal Atresias
- MYO5B-Related Progressive Familial Intrahepatic Cholestasis
- Myopathic Intestinal Pseudoobstruction
N7
- Neonatal Inflammatory Skin And Bowel Disease
- Neonatal Intrahepatic Cholestasis Due To Citrin Deficiency
- Neuroendocrine Tumor Of Pancreas
- Neurologic, Endocrine, And Pancreatic Disease, Multisystem, Infantile-Onset 1
- Neurologic, Endocrine, And Pancreatic Disease, Multisystem, Infantile-Onset 2
- NK-Cell Enteropathy
- Non-Functional Pancreatic Neuroendocrine Tumor
O1
P53
- Pancreatic Acinar Cell Carcinoma
- Pancreatic Acinar Cell Cystadenocarcinoma
- Pancreatic ACTH-Producing Neuroendocrine Tumor
- Pancreatic Adenocarcinoma
- Pancreatic Adenosquamous Carcinoma
- Pancreatic Agenesis
- Pancreatic Agenesis 1
- Pancreatic Agenesis 2
- Pancreatic Agenesis 3
- Pancreatic Cancer, Susceptibility To, 1
- Pancreatic Cancer, Susceptibility To, 2
- Pancreatic Cancer, Susceptibility To, 3
- Pancreatic Cancer, Susceptibility To, 4
- Pancreatic Cancer, Susceptibility To, 5
- Pancreatic Carcinoma With Mixed Differentiation
- Pancreatic Colipase Deficiency
- Pancreatic Cystadenocarcinoma
- Pancreatic Delta Cell Neuroendocrine Tumor
- Pancreatic Ductal Adenocarcinoma
- Pancreatic Endocrine Carcinoma
- Pancreatic Foamy Gland Adenocarcinoma
- Pancreatic Gastrin-Producing Neuroendocrine Tumor
- Pancreatic Gastrinoma
- Pancreatic Hypoplasia-Diabetes-Congenital Heart Disease Syndrome
- Pancreatic Insulin-Producing Neuroendocrine Tumor
- Pancreatic Insulinoma
- Pancreatic Intraductal Papillary-Mucinous Carcinoma
- Pancreatic Intraductal Papillary-Mucinous Neoplasm
- Pancreatic Intraductal Papillary-Mucinous Neoplasm With An Associated Invasive Carcinoma
- Pancreatic Large Cell Neuroendocrine Carcinoma
- Pancreatic Mucinous Cystadenocarcinoma
- Pancreatic Mucinous Cystadenoma
- Pancreatic Mucinous-Cystic Neoplasm With An Associated Invasive Carcinoma
- Pancreatic Neuroendocrine Neoplasm
- Pancreatic Neuroendocrine Tumor G1
- Pancreatic Non-Functioning Delta Cell Tumor
- Pancreatic Non-Invasive Mucinous Cystadenocarcinoma
- Pancreatic Serous Cystadenocarcinoma
- Pancreatic Signet Ring Cell Adenocarcinoma
- Pancreatic Small Cell Neuroendocrine Carcinoma
- Pancreatic Somatostatinoma
- Pancreatic Squamous Cell Carcinoma
- Pancreatic Triacylglycerol Lipase Deficiency
- Pancreatic Vasoactive Intestinal Peptide Producing Tumor
- Parenteral Nutrition-Associated Cholestasis
- Peutz-Jeghers Syndrome
- Polyps, Multiple And Recurrent Inflammatory Fibroid, Gastrointestinal
- PPoma
- Primary Intestinal Lymphangiectasia
- Progressive Familial Intrahepatic Cholestasis
- Progressive Familial Intrahepatic Cholestasis Type 1
- Progressive Familial Intrahepatic Cholestasis Type 2
- Progressive Familial Intrahepatic Cholestasis Type 3
S14
- Secondary Intestinal Lymphangiectasia
- Secondary Short Bowel Syndrome
- Short Bowel Syndrome
- Shwachman Syndrome
- Small Intestinal Fibrosarcoma
- Small Intestinal L-Cell Glucagon-Like Peptide Producing Tumor
- Small Intestinal Neuroendocrine Tumor G1
- Small Intestinal Sarcoma
- Small Intestinal Vasoactive Intestinal Peptide Producing Tumor
- Small Intestine Adenocarcinoma
- Small Intestine Neuroendocrine Neoplasm
- Spontaneous Intestinal Perforation
- Squamous Cell Carcinoma Of The Small Intestine
- Syndromic Congenital Sodium Diarrhea