Research conducted in a practice-based research network (PBRN) differs from other multisite research and presents particular planning challenges. The American Academy of Family Physicians National Research Network (AAFP NRN) has developed a number of procedures used for planning and implementing studies, which address the challenges of national PBRN studies. In this study, we highlight challenges common to PBRN research and describe the methods used by the AAFP NRN to address those challenges. The following tasks were identified as important to implementing PBRN research studies: (1) selecting fundable, feasible studies that interest members and have the potential to improve quality of care; (2) creating a practical budget that covers the costs of the study; (3) composing study teams and securing written agreements between team members; (4) recruiting and selecting study sites; and (5) training practice staff and physicians. Striking the balance of scientific rigor with practical application of PBRN studies must be addressed throughout these tasks. Proper planning for PBRN studies significantly affects the success of study implementation. Although developed by a national PBRN, the planning procedures described in this study may be adapted for state or regional PBRNs.