Background For optimal prosthetic anchoring in omarthritis surgery, a differentiated knowledge on the mineralisation distribution of the glenoid is important. However, database on the mineralisation of diseased joints and potential relations with glenoid angles is limited. Methods Shoulder specimens from ten female and nine male body donors with an average age of 81.5 years were investigated. Using 3D-CT-multiplanar reconstruction, glenoid inclination and retroversion angles were measured, and osteoarthritis signs graded. Computed Tomography-Osteoabsorptiometry (CT-OAM) is an established method to determine the subchondral bone plate mineralisation, which has been demonstrated to serve as marker for the long-term loading history of joints. Based on mineralisation distribution mappings of healthy shoulder specimens, physiological and different CT-OAM patterns were compared with glenoid angles. Results Osteoarthritis grades were 0-I in 52.6% of the 3D-CT-scans, grades II-III in 34.3%, and grade IV in 13.2%, with in females twice as frequently (45%) higher grades (III, IV) than in males (22%, III). The average inclination angle was 8.4°. In glenoids with inclination ≤10°, mineralisation was predominantly centrally distributed and tended to shift more cranially when the inclination raised to > 10°. The average retroversion angle was − 5.2°. A dorsally enhanced mineralisation distribution was found in glenoids with versions from − 15.9° to + 1.7°. A predominantly centrally distributed mineralisation was accompanied by a narrower range of retroversion angles between − 10° to − 0.4°. Conclusions This study is one of the first to combine CT-based analyses of glenoid angles and mineralisation distribution in an elderly population. The data set is limited to 19 individuals, however, indicates that superior inclination between 0° and 10°-15°, and dorsal version ranging between − 9° to − 3° may be predominantly associated with anterior and central mineralisation patterns previously classified as physiological for the shoulder joint. The current basic research findings may serve as basic data set for future studies addressing the glenoid geometry for treatment planning in omarthritis.