Aim To verify the accuracy of automatic image registration (IR) between the planning kilo voltage computed tomography (kV CT) and megavoltage cone beam computed tomography (MV CBCT) datasets using phantom and patient images. Background The automatic IR between MV CBCT and planning kV CT is a fast solution for performing online image guided radiotherapy (IGRT). The IR accuracy has to be verified periodically as it directly affects patient setup accuracy. Materials and methods The automatic IR accuracy was evaluated using image quality phantom acquired with different kV CT slice thickness, different MV CBCT acquisition MUs and reconstruction slice size and thickness. The IR accuracy was also evaluated on patient images on different anatomical sites such as brain, head & neck, thorax and pelvis. The uncertainty in the automatic registration was assessed by introducing known offset to kV CT dataset and compared with the registration results. Results The result with the phantom images was within 2 mm in all three translational directions. The accuracy in automatic IR using patient images was within 2 mm in most of the cases. 3 mm planning kV CT slice thickness was sufficient to perform automatic IR successfully within 2 mm accuracy. The MV CBCT reconstruction parameters such as slice thickness and slice size had no effect on the registration accuracy. Conclusion This study shows that the automatic IR is accurate within 2 mm and provides confidence in performing them between planning kV CT and MV CBCT image datasets for online image guided radiotherapy.