We investigated associations between full Electronic Medical Record (EMR) system adoption and drug use in healthcare organizations (HCOs) to explore whether EMR system features such as electronic prescribing, medicines reconciliation, and decision support, might be related to drug use by using the relevant nation-wide data.The study design was cross-sectional. Survey data of the level of adoption of EMR systems were collected for the Organization for Economic Co-operation and Development benchmarking information and communication technologies (ICT) study between November 2013 and January 2014, in Korea. Survey respondents were hospital chief information officers and medical practitioners in primary care clinics. From the national health insurance administrative dataset, two outcomes, the rate of antibiotic prescription and polypharmacy with ≥6 drugs, were extracted.We found that full EMR adoption showed a 16.1% lower antibiotic drug prescription than partial adoption including paper-based medical charts in the hospital only ( = 0.041). Between EMR adoption status and polypharmacy prescription, only those clinics which fully adopted EMR showed significant associations with higher polypharmacy prescriptions (36.9%, = 0.001).The findings suggested that there might be some confounding effects present and sophisticated ICT may provide some benefits to the quality of care even with some mixed results. Although a negative relationship between full EMR system adoption and antibiotic drug use was only significant in hospitals, EMR system functions searching drugs or listing specific patients might facilitate antibiotic drug use reduction. Positive relationships between full EMR system adoption and polypharmacy rate in general hospitals and clinics, but not hospitals, require further research.