BACKGROUND: Choosing which issues to discuss in the limited time available during primary care visits is an important task for complex patients with chronic conditions. DESIGN, SETTING, AND PARTICIPANTS: We conducted sequential interviews with complex patients (n = 40) and their primary care physicians (n = 17) from 3 different health systems to investigate how patients and physicians prepare for visits, how visit agendas are determined, and how discussion priorities are established during time-limited visits. KEY RESULTS: Visit flow and alignment were enhanced when both patients and physicians were effectively prepared before the visit, when the patient brought up highest-priority items first, the physician and patient worked together at the beginning of the visit to establish the visit agenda, and other team members contributed to agenda setting. A range of factors were identified that undermined the ability of patient and physicians to establish an efficient working agenda: the most prominent were time pressure and short visit lengths, but also included differing visit expectations, patient hesitancy to bring up embarrassing concerns, electronic medical record/documentation requirements, differences balancing current symptoms versus future medical risk, nonactionable items, differing philosophies about medications and lifestyle interventions, and difficulty by patients in prioritizing their top concerns. CONCLUSIONS: Primary care patients and their physicians adopt a range of different strategies to address the time constraints during visits. The primary factor that supported well-aligned visits was the ability for patients and physicians to proactively negotiate the visit agenda at the beginning of the visit. Efforts to optimize care within time-constrained systems should focus on helping patients more effectively prepare for visits. Physicians should ask for the patient's agenda early, explain visit parameters, establish a reasonable number of concerns that can be discussed, and collaborate on a plan to deal with concerns that cannot be addressed during the visit.