Tomotherapy (TomoTherapy, Inc., Madison, WI, USA) is a helical intensity modulated radiation therapy (IMRT) modality using rotational delivery of a fan beam like a CT scanner to deliver highly conformal radiation dose distributions in an intensity-modulated fashion. Tomotherapy can image guided radiation therapy (IGRT) using megavoltage computed tomography (MVCT). In this study, different CT slice thicknesses were acquired in order to evaluate the effect of CT slice thickness on tomotherapy planning and image registration for stereotactic body radio therapy (SBRT) or stereotactic radiosurgery (SRS) by using end-to-end (EtoE) phantom (Accuray, USA). EtoE phantom kilovoltage CT (KVCT) and MVCT images were acquired using CT (LightSpeed 16, GE, USA), and tomotherapy (Tomotherapy, USA), respectively. Reference planning target volumes (RPTV) in the EtoE phantom were contoured. The volume of the RPTV was 14.13 cc, and the CT image thicknesses were 2, 4, and 6 mm. CT images were planned based on the tomotherapy planning system (TPS), and all plans had the same constraints and iterations. The PTV volumes were 16.58 cc, 18.88 cc, and 20.28 cc in 2-, 4- and 6 mm planning KVCTs, respectively. The PTV volumes were 16.32, 18.00, and 22.04 cc in 2-, 4-, and 6 mm using MVCT, respectively. Heavy thickness planning of the CT slice overestimated the RPTV volume in TPS. Also, the heavy thickness MVCT image skipped target slice images. The target coverage of the treatment plans for different slice thicknesses was correlated with the tumor volume. At 10-Gy prescription dose of PTV, dose coverages of the reference planning target volume were 10.14, 10.25, and 10.27 Gy for 2-, 4-, and 6-mm slice thicknesses. Therefore, when radiosurgery is supplemented with tomotherapy, thin slice (<2 mm) planning should be done and MVCT images should be acquired