Background: This study was conducted to evaluate the factors affecting adherence in patients with hypertension and type 2 diabetes mellitus before and after a clinic based patient incentive program in Incheon. Methods: An observational follow-up study was done for 28,355 patients in one registered group and 245,598 patients in a non-registered group from March 16th 2009 to December 31th 2010 in Incheon. The registration, mandatory laboratory tests and number of clinic visits were collected by merging the Incheon Chronic Disease Management System data and the National Health Insurance Corporation (NHIC) data. As a measure of patient adherence, we used a variable of prescription days from the NHIC and defined above 80% of average prescription days as an appropriate patient adherence. Repeated measures analysis of variance and logistic regression were used to analyze the differences in patient adherence and factors affecting adherence. Results: The changes in prescription days for the registered group are larger than for the non-registered group. In the logistic regression model, including the variables with sex, age, income status and number of clinic visits, the registered group exhibited a higher Odds ratio in the patient adherence. Conclusion: This study revealed the association between registration and appropriate patient adherence in patients with hypertension or type 2 diabetes mellitus.