It is investigated to what extent EGM96 affects the accuracy of digital elevation model (DEM) produced from the shuttle radar topography mission (SRTM). Global and regional analysis of EGM96 compared with EGM2008 indicate that locally there are large differences distorting to the accuracy level of SRTM DEM. In the absolute sense, the overall geoid differences throughout arc-degree tiles reach −5 m in the northeast and 2–3 m in the southern parts of Turkey. A numerical investigation over the test profiles of 200–700 km length running at various directions proves that a possible vertical datum change from EGM96 to EGM2008 yields systematically more accurate height information with an improvement of up to 2.5 m. A GPS-levelling traverse of about 900 km length points out some key patterns of this recovery. Consequently, a correction for the present version of SRTM DEM should be considered in critical implementations of Earth sciences like geoid or water flow modelling, especially for areas where EGM96 shows weak performance.