Some prehistoric cranial and mandibular remains from Indonesia demonstrate the presence of tooth modification. This tradition seems to continue through the historical period and is still practiced in some regions. However, the pattern of dental modification was changed through time. The purpose of this study was to determine the long-term reasons behind the continuing tradition of dental modification in some communities, even though it is a tough and painful process. To do this, human skeletal remains from the prehistoric Eastern Indonesian archaeological sites of Liang Bua, Liang Toge, Lewoleba, Melolo and Pain Haka were analysed. These cave sites are all located within the Ngada Regency, Flores, where dental modification is still practiced. Through macroscopic observation the morphology of modifications on teeth was recorded and compared with the techniques and results of contemporary tooth modifications in the Ngada community. The results indicate cultural continuity with tooth modification practices revolving around initiation, maturity, and ethnic sustainability.