Recent advancements in Augmented (AR) and Mixed Reality (MR) have significantly impacted the orthopedic field, with hope of holographic tools to enhance surgical precision. This study explores the reliability of a specifically designed software tool, integrated with HoloLens, for measuring anatomical structures of the shoulder girdle in orthopedic surgery. Forty-two right scapulas were analyzed using CT scans, further converted into 3D models, which were then visualized as holograms and measured through augmented reality tools using the RSQ HOLO system. Three researchers performed measurements on three key distances: Glenoid Height (GH), Glenoid Width (GW), and Scapular Width (SW), across two sessions with a minimum 7-day interval. Statistical analysis using Intraclass Correlation Coefficient (ICC) revealed excellent intra-rater reliability for SW (0.96) and GW (0.91), and good reliability for GH (0.85). Inter-rater reliability also showed promising results, particularly for SW (0.91) and GW (0.78), although GH (0.72) showed moderate agreement. Descriptive statistics indicated minimal measurement differences across all groups, with the majority of differences being under 1 mm. These findings demonstrate holographic assessment of bone morphology is highly reliable, supporting its potential use in preoperative planning and intraoperative navigation. Further studies are needed to evaluate the software’s performance in clinical settings and its comparison with physical and CT measurements.