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Introduction: Many primary care patients with multimorbidity (two or more chronic conditions) and depression or anxiety have day-to-day challenges that affect health outcomes, such as having financial or housing concerns, or dealing with social or emotional stressors. Yet, primary care providers (PCPs) are often unaware of patients' daily challenges coping with chronic disease. We developed Customized Care, an intervention, to address the barriers to effective communication about patient's day-to-day challenges. Methods: In this report we describe the rationale and design of a randomized clinical pilot study to examine the effect of Customized Care on patient-PCP communication and patient health outcomes, including depression, anxiety and functional outcomes. Customized Care comprises two components: (1) a computer-based discussion prioritization tool (DPT) designed to empower patients to communicate their health related priorities; and (2) a customized question prompt list (QPL) tailored to these priorities. Primary care clinic patients and PCPs participated in the study, which consisted of in-person patient assessments, audio recording and transcription of the patient-PCP office visit, and follow-up patient assessments by phone. Results: We describe study participant demographics and development of a coding manual to assess communication within the office visit. Participants were recruited from an urban primary care clinic. Sixty patients and 12 PCPs were enrolled over six months. Conclusions: With better communication about everyday challenges, patients and PCPs can have more informed discussions about health care options that positively influence patient outcomes. We expect that Customized Care will improve patient-PCP communication about day-to-day challenges, which can lead to better health outcomes.