Abstract Background Medical records that do not accurately reflect the patient’s current medication list are an open invitation to errors and may compromise patient safety. Methods This cross-sectional study compares primary care provider (PCP) medication lists and pharmacy claims for 100 patients seen in 8 primary care practices and examines the association of congruence with demographic, clinical, and practice characteristics. Medication list congruence was measured as agreement of pharmacy claims with the entire PCP chart, including current medication list, visit notes, and correspondence sections. Results Congruence between pharmacy claims and the PCP chart was 65%. Congruence was associated with large chronic disease burden, frequent PCP visits, group practice, and patient age ≥45 years. Conclusion Agreement of medication lists between the PCP chart and pharmacy records is low. Medication documentation was more accurate among patients who have more chronic conditions, those who have frequent PCP visits, those whose practice has multiple providers, and those at least 45 years of age. Improved congruence among patients with multiple chronic conditions and in group practices may reflect more frequent visits and reviews by providers.