The primary objective of this study was to investigate the biomechanical effects and stresses on bone, periodontal ligament (PDL), cementum and displacement along X-, Y- and Z-axis during true intrusion of incisors using mini-implants with Finite Element Analysis; the secondary objective of the study was to find out the best method for anterior intrusion in clinical practice to treat anterior deep bite malocclusions. A 3D finite element method was used to simulate true anterior intrusion with sliding mechanics using mini-implants. Two groups were modelled with mini-implants placed distal to lateral incisors for Model1, and below the anteriornasalspine (ANS) for Model2, to achieve intrusion. von Mises stress, principal stress on PDL and alveolar bone, displacements in all 3 planes were determined. Amongst the modalities compared in the present study, the stresses on bone and PDL were showing best behavior for mini-implants placed distal to lateral incisors (Model1). The teeth showed controlled tooth movement in Model1. Maximum stress was found in the cortical bone and in the PDL. Nature of the stress changed from compressive to tensile from cervical area to root apex, concentrating mainly at the apical area. Amongst the modalities compared, the best controlled tooth movements for anterior intrusion to treat anterior deep bite malocclusions, was for mini-implants placed distal to lateral incisors (Model1).