Adult stem cell (ASC)-derived organoid cultures have become an important model system for studying mammalian epithelial tissues in health and disease, including autoimmune conditions. Somatic stem cells are isolated and embedded into basement membrane-like matrix to allow for the in vitro outgrowth of miniature versions of functional epithelium in the presence of supportive growth factor niche. Organoids derived from tissues affected by autoimmune diseases, such as the intestine in inflammatory bowel disease or salivary glands in Sjögren’s disease, may provide an invaluable platform for exploring disease mechanisms, immune-epithelial interactions, and therapeutic interventions. Here, we describe the basic establishment and maintenance principles of mouse intestinal organoid cultures, suitable for many downstream applications, including for disease modeling, drug discovery, and regenerative medicine.