Understanding the mechanism of action of pharmacologic agents allows the practitioner to rationally use them. This two-part review of clinical pharmacology attempts to address the chemical nature and action of drugs commonly used in gastrointestinal practice. Part I reviews agents used in the endoscopy laboratory for premedication and prophylaxis for infection. Part II will review the pharmacology of agents used in the daily practice of gastroenterology including antacids, H2 and proton pump blockers, cytoprotection agents, pancreatic enzymes, drugs for dissolution of gallstones, prokinetic agents, anti-inflammatory agents for inflammatory bowel disease, and drugs for symptomatic treatment of functional bowel complaints.