There are several methods for estimating IR and β-cell dysfunction for prediction of type 2 diabetes mellitus (T2DM). The original HOMA (HOMA1) is not always reliable because of the variations in the glucose resistance of the peripheral tissue and liver. An updated HOMA (HOMA2) recalibrated the variations mentioned above was announced and HOMA2 has been used to study for predictive marker of T2DM in diverse ethnic groups. But there is no a study of the correlation between HOMA2 and HOMA1 and the development of overt diabetes. The aim of this study is to compare the usefulness of HOMA1 and HOMA2 for predicting progression to diabetes in Koreans. Retrospective observational study of participants in a health checkup was designed. The subjects who had history of diabetes or were taking oral hypoglycemic agents were excluded and a final study population was 104,694 Koreans. The subjects were divided by normal glucose tolerance (NGT) group and pre-diabetes group. The primary purpose of study was to compare the predictive ability of HOMA1 and HOMA2 for T2DM, so the hazard ratios (HRs) of the HOMA values were calculated. HOMA1 and HOMA2 were compared for independent incident diabetes development by use of HRs from multivariable Cox proportional hazards models. In this study, both HOMA1-IR and HOMA2-IR were statistically significant markers for predicting the development of T2DM in the NGT Korean group, and especially, HOMA2-β was the potential marker for predicting the future development of T2DM in the non-diabetic Korean group by compared with HRs.