Pharmaceutical profiling is the characterization of the physicochemical and metabolic properties of compounds during drug discovery. The data alerts project teams to compound liabilities, helps to diagnose complex in vivo processes such as bioavailability, helps to better plan and interpret discovery experiments, and provides feedback for synthetic chemical modifications to the structure that are designed to improve properties. Automation plays an important role in obtaining diverse sets of property data for thousands of compounds per year with short turnaround times that match discovery workflow. Key elements of automation in profiling include liquid handling, high capacity detection, and data processing and reporting. Key information is obtained from high throughput assays for integrity, permeability, solubility, stability, cytochrome P450 inhibition, lipophilicity, and pKa. Automated assays for these properties are discussed.