Inclusion Criteria:
* Male or non-pregnant, non-lactating females, 18-80 years old years of age
* Females of childbearing potential must be taking adequate contraceptive precautions (i.e., implants, injectables, hormonal intrauterine devices, combined hormonal contraceptives, having a vasectomized partner or total abstinence from heterosexual relations with no plans of becoming pregnant through insemination or in vitro fertilization) and have a negative urine pregnancy test prior to randomization.
* Active symptoms of MC defined by non-bloody, watery diarrhea or loose bowel movements for at least 12 weeks (for patients with newly diagnosed MC) or a history of clinical relapse for at least one week before randomization in patients with previously established MC, and with \>=28 stools within 7 days preceding randomization, of which \>=20 were watery/soft stools
* Colonoscopy or flexible sigmoidoscopy with histologically confirmed MC, defined by signs of inflammation of the lamina propria and either:
* lymphocytic colitis: ≥20 IELs/100 surface epithelial cells
* collagenous colitis: subepithelial collagen band \>10 micrometers in diameter
* Ability of subject to participate fully in all aspects of this clinical trial
* Written informed consent must be obtained and documented
Exclusion Criteria:
* Evidence of infectious diarrhea (proved by stool culture or colonic biopsy), diarrhea due to other organic diseases of the gastrointestinal tract including Crohn's disease, ulcerative colitis, ischemic colitis, Celiac disease (ruled out by either duodenal biopsy or serum antibodies), radiation colitis, or polyps \>2cm, suspicion of drug-induced MC
* History of partial or total colonic resection
* Previous exposure to \>7 days of any budesonide formulation for treatment of MC
* Unwillingness to withhold protocol-proscribed medications during the trial
* Received any of: aminosalicylates, corticosteroids (other than budesonide), immunosuppressants (including thiopurines and methotrexate), bismuth subsalicylate, cholestyramine, biological treatments, or antibiotics (except for up to a 7-day course for conditions unrelated to microscopic colitis) within 8 weeks of randomization
* Use of loperamide or diphenoxylate/atropine as an anti-diarrheal agent is not permitted during the screening period
* Serious underlying disease other than MC which in the opinion of the investigator may interfere with the subject's ability to participate fully in the study, including a history of:
* Severe anaemia (haemoglobin \< 90 g/L) or leukopenia (white blood cell count \< 2.5 x 109 cells/L)
* Known infection with hepatitis B, hepatitis C, or human immunodeficiency virus not on effective anti-viral therapy
* Active malignancy
* Cirrhosis or significant hepatic or renal insufficiency
* Poorly controlled type 1 or type 2 diabetes
* Glaucoma
* History of alcohol or drug abuse which in the opinion of the investigator may interfere with the subject's ability to comply with the study procedures.
* Pregnant or lactating women
* Hypersensitivity to the active ingredient of budesonide MMX® or budesonide CR and excipients
