The hypothesis of this study is that an altered gut microbiota is a contributory factor in initiating an inflammatory process in the colonic mucosa leading to collagenous colitis. The investigators suggest that treatment with budesonide reduces the inflammation without treating the underlying cause. In this trial the investigators will try to modullate gut microbiota by adding rifaximin. The aim of this study is to assess if 4 weeks treatment with rifaximin as a supplement to a standard course of budesonide against active CC can reduce the risk of relapse after treatment cessation.

Patients with biopsy-verified CC and active disease defined by >3 bowel movements/day or >1 watery stool measured as a mean for a week. Patients will be invited to participate in the study independently of age and disease duration.

Inclusion Criteria:

• • Signed informed consent

  • Histological findings fulfill criteria for CC:

    • A subepithelial collagenous band >10 μm in colonic biopsies
    • Increased count of inflammatory cells in lamina propria

  • Diagnostic biopsies are a maximum of two years old

  • A history of nonbloody, watery diarrhea for more than two weeks prior to screening in patients with recently diagnosed CC or a history of clinical relapse for more than a week in patients with known CC

  • Active disease: > 3 stools/day or >1 watery stool/day measured as a mean during a week prior to baseline

Exclusion Criteria:

• - Significant findings at colonoscopy that could cause diarrhea (colonic diverticulosis and polyps < 2 cm are not considered significant findings)
• Biopsies more than two years old in a patient, who does not accept a new sigmoidoscopy
• Untreated celiac disease
• Positive stool cultures for pathogenic intestinal bacteria including Clostridium difficile
• Suspected colitis induced by medication (diarrhea shortly after commencement of NSAID's, statins, SSRI or PPI)
• Severe comorbidity (cardiovascular, renal, endocrine, neurologic, pulmonal or psychiatric) or history of cancer during the last 5 years
• Abnormal liver biochemistry (ALAT or ALP > 2,5 x upper limit), cirrhosis or portal hypertension
• Pregnancy or lactation (assured by negative P-hCG at inclusion)
• History of significant intestinal resection
• Treatment with 5-ASA, Salazopyrin, immunemudulators (Azathioprine, 6-mercaptopurine or Methotrexate), biologic drugs (TNF-alfa-inhibitors), local or systemic glucocorticoids (except for Budesonide) within the last three month
• Allergy or intolerance to Rifaximin (or similar antibiotics such as Rifampicin or Rifabutin)
• Expectation of lack of cooperation or insufficient comprehension
• Concomitant participation in an other clinical trial or participation within the last 30 days
• Patients receiving Warfarin or Marcoumar (interaction with risk of uncontrolled INR-levels)

De-identified individual participant data for all primary and secondary outcome measures will be made available

Within 6 months of study completion

Requestors will be required to sign a Data Access Agreement

Randomisation and labelling follow guidelines defined by the Danish Medicines Agency and will be performed by the Hospital Pharmacy Region Midtjylland Clinical Trial Unit, Aarhus University Hospital and Norgine. For equal allocation to the two treatment arms computer generated block randomisation (blocks of 8) will be performed