BACKGROUND: Researchers have the potential to utilize genetic modification (GM) technologies to create a hybrid of "food" and "medicine" that may challenge traditional understandings of what is "natural". Moral and ethical concerns are likely to arise in any discussion of these therapeutic foods and will affect the integration of products into clinical care and daily life. This study examined how patients with chronic gastrointestinal (GI) diseases view probiotics as future bioengineered therapeutic foods. METHODS: A multi-site qualitative study consisting of focus groups with chronic GI diseases was conducted at Cleveland Clinic, Mayo Clinic, and Johns Hopkins University RESULTS: We conducted twenty-two focus groups with 136 patients with major GI diseases between March and August 2009. GI patients associated the term "natural" with concepts of diminished risk and morally "good"; conversely, patients associated the term "unnatural" with things that are "risky," "foreign", and morally "bad". Readily available unmodified probiotics were more commonly described as "natural" while genetically modified probiotics were more commonly labeled as "unnatural" and "risky". However, patients acknowledged that not all natural products are safe, nor are unnatural products always harmful. CONCLUSIONS: If GI patient perspectives are indicative of public perceptions of therapeutic foods, our findings suggest that the potential benefits and risks of clinical and public health initiatives employing therapeutic foods will be understood in moralistic terms. Bioethicists and others should be sensitive to the implicit normative appeals that are often embedded in the language of what is "natural" and "unnatural".