Background: As most of people in Korea are covered by National Health Insurance (NHI), the disease information collected in NHI provides high availability for health policy. Nevertheless, the validity of disease codes in NHI data has been controversial till now. So we tried to evaluate the validity of them by comparing the NHI claims data with Korean National Hospital Discharge In-depth Injury Survey (KNHDIIS) data. Methods: We compared the NHI patients sample data (2009) with the KNHDIIS data (2009). We selected the inpatient data of KNHDIIS and NHI patients sample. The weighted number of patients from NHI patients sample was 5,551,210 and the number of patients from KNHDIIS was 5,559,874. We classified the disease codes into principal diagnoses and other diagnoses, and we compared as one, two, three unit level. Also we calculated the agreement rate of each of them. Results: In the comparison of principal diagnoses, NHI claims data had more C code than KNHDIIS data did, whereas KNHDIIS data had more Z code than NHI claims data did. In the comparison of other diagnoses, NHI claims data had 2, 3 more codes than KNHDIIS data did. The overall agreement rate at three unit level was 76.5% in principal diagnoses and 46.8% in other diagnoses. Conclusion: Considering the large difference between the two data, the validity of disease codes in NHI Claims data seems to be low. To increase the validity of them, the definite detail coding indicator, the reinforcement of coding education, and the reform of system are needed.