Systemic mast cell disease often becomes clinically manifest as a mast cell mediator activation syndrome with episodic or chronic nonspecific abdominal symptoms. As a result of genetic alterations, pathological mast cells have an increased proliferation rate as well as accumulation within different organs with consequential effect on gastrointestinal secretion, absorption, pain perception and motility caused by release of their mediators. These changes may not be detected in routine laboratory or imaging methods. This report describes how the diagnosis systemic mast cell disease can be established with a diagnostic questionnaire based on a synopsis of clinical findings relevant to a mast cell mediator activation syndrome.