The purpose of this study was to evaluate in vivo fit and fill analysis of tapered wedge-type stem in total hip arthroplasty (THA) with computed tomography (CT)-based navigation system. 100 THAs were all performed through the posterolateral approach, with patients in the lateral decubitus position. Each cohort of 50 consecutive primary cementless THAs with was compared with and without CT-based navigation system. The post-operative antero-posterior (AP) hip radiographs were obtained two weeks after the operation. All radiographic fit and fill measurements in the proximal and distal areas were analyzed by two of the authors who were both blinded to the use of CT-based navigation system. The type of the fit in the cementless stem was divided into three types. The fit of the stem was classified as Type I, if there was both proximal and distal engagement (maximum proximal to distal engagement difference of 2 mm or greater), Type II when there was proximal engagement only, and Type III when there was distal engagement only. The fill parameters such as mean stem-to-canal ratios and mean minimum and maximum gaps between the stems to the cortical bone in proximal and distal sections were compared. There was a significantly better overall canal fit obtained by THA with CT-based navigation system compared to without the navigation system (p<0.01). With CT-based navigation system, 42 of 50 stems (84%) were categorized as Type I fit compared to 31 of 50 stems (62%) without the navigation system. As to Type II fit, There are significantly more stems without the navigation system (26%) compared to with it (12%). There were better canal fills of the stems obtained by THA with CT-based navigation system both in proximal (94%) and distal sections (88%) of the femur compared to without the navigation system (proximal 88%/distal 82%) (p<0.05). Excellent radiographic fit and fill has been previously reported to potentially correlate with improved clinical outcomes. The stems obtained by THA with CT-based navigation system had a significantly better canal fit demonstrated by higher proportion of Type I and lower proportion of Type II fits, compared to without the navigation system. The stems with the navigation system had also significantly better proximal and distal canal fill.