Statement of the problem: In implant dentistry literature, the most commonly investigated materials/structures in finite element analysis studies are either implant, peri-implant bone (cortical and cancellous bone), and restoration. This method allows application of simulated forces at specific points in the system and analysis of stress in the implant and peri-implant region. The implant connection design and other factors as the prosthesis type, its height and material have a great effect on stresses falling on the bone around implant Objectives: to evaluate and compare stress distribution using (3dimensional) finite element analysis between implants with Internal Hex and Morse Taper connections that were simulated in bone without vertical defect and with 6 mm vertical defect. Material and methods: In this study, the implants examined were titanium implants with Morse taper and internal hex connections. These implants were utilized in the two configurations that were designed in this study. In the first configuration, the jawbone has no vertical defect and composed of (starting from top down) one mm layer of crestal cortical bone, 3.5 mm layer of cancellous bone, 0.5 mm sinus cortical bone. In the second configuration, it is composed of (starting from top down) one mm layer of crestal cortical bone, 3.5 mm layer of cancellous bone, 0.5 mm sinus cortical bone with a 6 mm vertical bone defect was created. The force of 100N is applied in axial, oblique and axial and oblique directions. Stresses falling on surrounding bone, fixture, abutment and screw were analyzed using finite element analysis in the two different configurations. Results: The maximum Von Mises stresses for different loading conditions were recorded at different areas of the implant abutment assembly and in the surrounding bone and it was found that in all direction of forces, the stress levels falling on the bone, abutment, fixture and screw were more in the bone defect configuration than the models with no bone defects.In all direction of forces, the implants with Morse taper abutments showed less stress on the fixture compared to internal hex abutments in both models with and without defect. Conclusion: Morse taper connections showed less stresses on the bone, fixture, abutment and screw than the internal Hex connection regardless of the bone height. Furthermore, stress distribution was more with implant in the 6 mm vertical defect than that in the bone without defect.