Purpose A possible complication after total disc replacement (TDR) is subsidence, presumably caused by asymmetric implantation, implant undersizing or reduced bone quality. This study aims to quantify the degree of subsidence of an SB Charité TDR, and investigate whether undersizing is related to subsidence. Methods A custom developed software package (Mathworks) reconstructed 3D bone-implant geometry. A threshold for subsidence was determined by comparing penetrated bone volume (PBV) and rotation angles. Inter- and intra-observer reproducibilities were calculated. Subsidence was correlated to undersizing. Results High inter- and intra-observer correlation coefficients were found for the method (R > 0.92). Subsidence was quantified as PBV 700 mm3 combined with a rotation angle >7.5°. A reduced risk of subsidence was correlated to >60 and >62 % of the bony endplate covered by the TDR endplate for L4 and L5, respectively. Conclusions A reproducible method to determine undersizing was developed. Thresholds were determined related to a reduced risk of subsidence.