While more than 3,000 salivary proteins have been identified since the early 2000s, there has not been any trial to build Korean saliva proteome. Additionally, ethnic differences in the human plasma proteome were recently reported, but there was not any report on this aspect in the human saliva proteome, yet. Thus, here, the Korean whole saliva (WS) proteome was constructed for the first time and it was characterized by the comparison with the integrated human saliva protein dataset for the determination of ethnic differences in the human saliva proteome. A total of 674 proteins were indexed in the catalogue by the nLC-Q-IMS-TOF analyses of WS samples collected from 11 healthy South Korean adult male volunteers and 11 healthy South Korean adult female volunteers. Among 674 proteins, 358 proteins were not found in the integrated human saliva protein dataset. Also, the significant uniqueness of the Korean WS proteome was observed in gene ontology. Since the inter-platform reproducibility of the nLC-Q-IMS-TOF system was confirmed, these observations are strong evidences to support ethnic differences in the human saliva proteome. Additionally, since 47 out of the 358 distinct Korean WS proteins were found to be associated with the top 10 deadliest diseases in South Korea, the potential of ethnicity-specific human saliva proteins as biomarkers for diseases highly prevalent in that ethnic group was confirmed. Finally, the present Korean WS protein catalogue is expected to be used as the first level reference for future Korean saliva proteome studies.