Primary care practices play a vital role in healthcare delivery since they are the first point of contact for most patients, and provide health prevention, counseling, education, diagnosis and treatment. Practices, however, face a complex appointment scheduling problem because of the variety of patient conditions, the mix of appointment types, the uncertain service times with providers and non-provider staff (nurses/medical assistants), and no-show rates which all compound into a highly variable and unpredictable flow of patients. The end result is an imbalance between provider idle time and patient waiting time. To understand the realities of the scheduling problem we analyze empirical data collected from a family medicine practice in Massachusetts. We study the complete chronology of patient flow on nine different workdays and identify the main patient types and sources of inefficiency. Our findings include an easy-to-identify patient classification, and the need to focus on the effective coordination between nurse and provider steps. We incorporate these findings in an empirically driven stochastic integer programming model that optimizes appointment times and patient sequences given three well-differentiated appointment types. The model considers a session of consecutive appointments for a single-provider primary care practice where one nurse and one provider see the patients. We then extend the integer programming model to account for multiple resources, two nurses and two providers, since we have observed that such team primary care practices are common in the course of our data collection study. In these practices, nurses prepare patients for the providers’ appointments as a team, while providers are dedicated to their own patients to ensure continuity of care. Our analysis focuses on finding the value of nurse flexibility and understanding the interaction between the schedules of the two providers. The team practice leads us to a challenging and novel multi step multi-resource mixed integer stochastic scheduling formulation, as well as methods to tackle the ensuing computational challenge. We also develop an Excel scheduling tool for both single provider and team practices to explore the performance of different schedules in real time. Overall, the main objective of the dissertation is to provide easy-to-implement scheduling guidelines for primary care practices using both an empirically driven stochastic optimization model and a simulation tool.