This paper presents the cognitive model of gastroesophageal reflux disease (GERD) developed for the Maryland Virtual Patient simulation and mentoring environment. GERD represents a class of diseases that have a large number of clinical manifestations. Our model at once manages that complexity while offering robust automatic function in response to open-ended user actions. This ontologically grounded model is largely based on script-oriented representations of causal chains reflecting the actual physiological processes in virtual patients. A detailed description of the GERD model is presented along with a high-level description of the environment for which it was developed.