The chronic disease management program (CDMP), a multilevel intervention including copayment reduction and physician incentives, was introduced in 2012 in Korea to improve blood pressure and glycemic control by strengthening the function of clinic as primary care institutions in managing hypertension and diabetes. This study, therefore, aimed to evaluate the effect of CDMP on the appropriateness of medication adherence and persistence in hypertension or type-2 diabetes patients.A pre-post retrospective study was conducted using claims cohort data from 2010 to 2013. Hypertension or type-2 diabetes patients were selected as the CDMP group, while dyslipidemia patients were the control group. Study groups were further categorized as clinic shifters or non-shifters on the basis of whether hospital use changed to clinic use during the study period. Prepost changes in adherence and persistence were assessed. Adherence was measured by medication possession ratio (MPR) and categorized as under (<0.8), appropriate (0.8-1.1), and over-adherence (>1.1). Persistence was measured by 12-month cumulative persistence rate.The pre-post change was significantly improved for appropriate-adherence (hypertension, +6.0%p; diabetes, +6.1%p), 12-month cumulative persistence (hypertension, +6.5%p; diabetes, +10.8%p), and over-adherence (hypertension, À5.3%p; diabetes, À2.8% p) only among the shifters in the CDMP group. Among these, patients visiting the same, single clinic showed a significant increase in appropriate-adherence, whereas those who changed their clinics showed a nonsignificant increase. No significant improvement was verified among the non-shifters in the CDMP group.CDMP improved medication adherence and persistence by significantly increasing appropriate-adherence and 12-month cumulative persistence rate in hypertension and type-2 diabetes patients. Particularly, CDMP significantly improved over-adherence, which was associated with increasing healthcare costs and hospitalization risk.Abbreviations: AHDs = antihypertensive drugs, BP = blood pressure, CDMP = chronic disease management program, COC = continuity of care, COCI = continuity of care index, CVD = cardiovascular disease, HbA1c = hemoglobin A1c, KNHIS-NSC = Korea National Health Insurance Service-National Sample Cohort, LLDs = lipid-lowering drugs, MPR = medication possession ratio, OADs = oral antidiabetes drugs, PDC = proportion of days covered, UPI = usual provider continuity index.