Geoid heights are important for converting terrain elevation from one reference system to another. Different space agencies have developed digital elevation model (DEM) products, which are commercially as well as accessible openly for the earth or its regions in different vertical datums. These DEMs are commonly available in either EGM96 or WGS84 datum. The shape of the geoid(s) developed over time have been derived using approximation of spherical harmonics. Geoid height plays an important role during comparison, validation and utilization of these DEMs. In this study, geoid heights (N) were calculated for EGM84, EGM96 and EGM 2008 using GeographicLib online service at locations of ground control points (GCPs) and analyzed. The mean geoid undulation for the three sites at Kendrapara, Orissa; Jaipur, Rajasthan and Dehradun, Uttarakhand are -62.92m, -50.24m and -44.02m respectively. Whereas the standard deviation for the three sites at Kendrapara, Orissa; Jaipur, Rajasthan and Dehradun, Uttarakhand are 0.27m, 0.46m and 1.22m respectively. The negative values of geoid heights in all the three experimental sites depicts negative gravity anomaly i.e. mass deficit, at these sites and thus indicating that in these regions the surface of the geoid is lower than the reference ellipsoid (WGS84). The resulting standard deviations also depict the increasing roughness of the experimental sites in the order: Kendrapara site, Jaipur site to maximum at Dehradun site.