The use of drugs to integrate basic and clinical sciences is frequently used in a lecture format, but the availability of alternative pedagogical approaches that address higher-order learning are not widely available. The use of case studies and case-based projects to reinforce lectures can help link basic and clinical disciplines and promote knowledge retention. Case based projects also help students with varying levels of background education see the applicability of topic material, and this may maintain engagement. However, both the significant time and effort and the general breadth of knowledge across basic science content areas necessary to construct clinically relevant basic science cases may serve as hindrances to their development. To address this issue, the author designed an integrated case that uses proton pump inhibitors (PPIs) to connect basic pharmacological principles with basic gastrointestinal physiology and pathophysiology. The development of this case grew out of discussions with clinical faculty members and students regarding general confusion surrounding how and why drugs that act in the stomach on parietal cells are made as enterically coated prodrugs to protect them from destruction by stomach acid. Thus, in the process of searching the literature to resolve this paradox, it became apparent that this would be an excellent way to connect gastrointestinal physiology, pharmacology, and biochemistry. In an effort to link physiology and pharmacology together in a vertical fashion, a case study was designed using the mechanism of action of PPIs and GERD as a unifying element. In the first module, the intent was to use a clinically relevant case study to highlight the importance of drug delivery, ion trapping, formulation, and drug-receptor interactions with gastrointestinal physiology. In the second module, the goal was to use the same case to highlight and review key aspects of gastric acid secretion and regulation.