Establishing regional infection control units is vital for effective national infection control. Therefore, an in-depth segmentation strategy is required. The annual incidence rates of Korea national notifiable infectious diseases in 16 different regions from 2001 to 2016 were analyzed using K-means clustering. Four clusters from non-normalized and normalized analyses were obtained for the annual incidence rates of these diseases by region. This study demonstrates the possibility of developing objective and reproducible approaches to regional segmentation for national infection control.