Objectives To understand the extent to which behaviors consistent with high quality medication reconciliation occurred in primary care settings and explore barriers to high quality medication reconciliation. Design Fully mixed sequential equal status design including ethnographic observations, semi-structured interviews, and surveys. Setting Primary care practices within an integrated healthcare delivery system in the United States. Participants We conducted 170 observations of patient encounters across 15 primary care clinics, 48 semi-structured interviews with staff, and 10 semi-structured interviews with patients. We also sent out surveys to 2,541 eligible staff with 616 responses (24% response rate) and to 5,132 eligible patients with 577 responses (11% response rate). Results Inconsistency emerged as a major barrier to effective medication reconciliation. This inconsistency was present across a variety of factors such as the lack of standardized workflows for conducting medication reconciliation, a lack of knowledge about medication and the process of medication reconciliation, varying levels of importance ascribed to medication reconciliation, and inadequate integration of medication reconciliation into clinical workflows. Findings were generally consistent across all data collection methods. Conclusion We have identified several barriers which impact the process of medication reconciliation in primary care settings. Our key finding is that the process of medication reconciliation is plagued by inconsistencies which contribute to inaccurate medication lists. These inconsistencies can be broken down into several categories (standardization, knowledge, importance, and inadequate integration) which can be targets for future studies and interventions.