Restoration of the glenoid joint line in shoulder arthroplasty is important for implant positioning and function. Medialization of the glenohumeral joint line due to glenoid bone loss is commonly encountered in primary and revision of shoulder arthroplasty albeit the direction and location of bone loss varies with different pathology. Three-Dimensional (3D) planning software has assisted in preoperative planning of complex glenoid deformities. However, limited literature is available defining a reliable 3D method to evaluate the glenoid joint line preoperatively. The purpose of this study is to identify a set of reliable scapular landmarks to be used as reference points to measure the premorbid glenoid joint line using 3D segmented models of healthy scapulae. Bilateral computed tomography scans from 79 patients eligible for primary stabilization procedures were retrospectively selected from our institutional surgical database (mean age 35±10 years, 58 males and 21 females). 3D models of the contralateral healthy scapulae were created via computed tomography scan segmentation using Mimics 24.0 software (Materialise, Leuven, Belgium). Anatomical landmarks were identified using 3-Matic 16.0 software (Materialise, Leuven, Belgium). The distance between identified landmarks and a sagittal plane created on the deepest point of the glenoid was recorded for each scapula and reliability of each landmark was assessed. Inter- and intra-observer reliabilities were also evaluated using intraclass correlation coefficients (ICCs). Four landmarks showed statistically significant results: the scapular notch (SN), the centroid of the coracoid (CC), a point on the most medial border of the scapula in line with the scapular spine (TS), and the most lateral point of the acromion (AL). The mean (± standard deviation) joint line measured from the SN, CC, TS and AL were 28.36±2.97 mm, 11.66±2.07 mm, 107.52±8.1 mm, and 29.72±4.46 mm, respectively. Inter-observer reliability analysis for SN, TS, and AL showed excellent agreement with ICC values of 0.966, 0.997, and 0.944, respectively, and moderate agreement for CC with ICC of 0.728. The results from this study assist in estimating joint line medialization preoperatively and in planning its subsequent restoration. A set of reliable landmarks can be used as references to estimate the premorbid glenoid joint line preoperatively.