Purpose. There are several factors that may influence implant site preparation with implant design being a paramount factor; however, few studies investigate its impact. The purpose of the study was to explore the comparative efficacy of using two different drilling protocols using burs with different design for preparing implant sites, by evaluating radiographic and clinical outcomes. Materials and Methods. The present randomized controlled clinical trial with an allocation ratio of 1:1 was carried on in two private practice offices by two experienced surgeons and researchers. In the control group the surgeons followed the protocol with standard straight burs while in the test group they used step burs. In both groups the patients received the same type of implants and prosthesis. The primary outcome was the marginal bone resorption one year after the prosthetic placement. Results. In the study were included and treated a total of 60 subjects (86 implants). At the one-year follow-up were screened 54 subjects (74 implants), and 50 at the 2-year follow-up (69 implants). This study showed no evidence of a difference in bone resorption, which increased significantly over time, between the two groups. Conclusions. Both clinical parameters and patientcentered outcomes revealed no difference between the two protocols of implant site preparation with two different drill shape.