There are many published reports demonstrating the accuracy of CT-based navigation systems. However, the use of such systems often subjects patients to a high level of radiation exposure. CT scans acquired using thinner slices are considered to lead to more accurate results, but also increase radiation exposure. We took the postoperative CT scans for 56 cases of total hip arthroplasty performed using a CT-based navigation system and analyzed the accuracy of the cup and stem positioning. Of these cases, 41 were performed using 3-mm CT slices and 15 were performed using 1-mm slices, enabling us to compare the accuracy of the system and the radiation exposure using the different slice thicknesses.CT-based navigation appears to be very accurate with regard to cup anteversion and leg length, but inaccurate with regard to stem anteversion. As for the varus/valgus angle of the stem, the navigated approach seems to be very accurate in terms of the numerical value, but this does not satisfy us: Stem anteversion is still inaccurate with this system, while cup inclination is sufficiently accurate with both navigation and manual methods.Use of 1-mm CT slices results in twice the radiation exposure associated with 3-mm CT slices, but there is little difference with respect to accuracy. It is therefore recommended to use a CT-based navigation system with 3-mm CT slices for accurate and safe total hip arthroplasty.