Collagenous gastritis, without colonic involvement, is exceptionally rare. It is not known to be associated with IgA deficiency and scleroderma. This is the first report of this type of association. We present a 26-year-old white female with a past medical history of gastroesophageal reflux disease and scleroderma. She was evaluated for complaints of abdominal pain and diarrhea. Esophagogastroduodenoscopy showed gastritis and duodenitis. Colonoscopy was normal. The histopathological report showed collagenous gastritis and focal lymphocytic duodenitis. A definitive treatment has not been established for this condition. Reporting such cases furthers understanding of the disease and will help to establish diagnostic criteria and to develop therapeutic strategies.