Glenoid and humeral head bone defects have long been recognized as major determinants in recurrent shoulder instability as well as main predictors of outcomes after surgical stabilization. However, a universally accepted method to quantify them is not available yet. The purpose of the present study is to describe a new CT method to quantify bipolar bone defects volume on a virtually generated 3D model and to evaluate its reproducibility. A cross-sectional observational study has been conducted. Forty CT scans of both shoulders were randomly selected from a series of exams previously acquired on patients affected by anterior shoulder instability. Inclusion criterion was unilateral anterior shoulder instability with at least one episode of dislocation. Exclusion criteria were: bilateral shoulder instability; posterior or multidirectional instability, previous fractures and/or surgery to both shoulders; congenital or acquired inflammatory, neurological, or degenerative diseases. For all patients, CT exams of both shoulders were acquired at the same time following a standardized imaging protocol. The CT data sets were analysed on a standard desktop PC using the software 3D Slicer. Computer-based reconstruction of the Hill-Sachs and glenoid bone defect were performed through Boolean subtraction of the affected side from the contralateral one, resulting in a virtually generated bone fragment accurately fitting the defect. The volume of the bone fragments was then calculated. All measurements were conducted by two fellowship-trained orthopaedic shoulder surgeons. Each measurement was performed twice by one observer to assess intra-observer reliability. Inter and intra-observer reliability were calculated. Intraclass Correlation Coefficients (ICC) were calculated using a two-way random effect model and evaluation of absolute agreement. Confidence intervals (CI) were calculated at 95% confidence level for reliability coefficients. Reliability values range from 0 (no agreement) to 1 (maximum agreement). The study included 34 males and 6 females. Mean age (+ SD) of patients was 36.7 + 10.10 years (range: 25 – 73 years). A bipolar bone defect was observed in all cases. Reliability of humeral head bone fragment measurements showed excellent intra-observer agreement (ICC: 0.92, CI 95%: 0.85 – 0.96) and very good interobserver agreement (ICC: 0.89, CI 95%: 0.80 – 0.94). Similarly, glenoid bone loss measurement resulted in excellent intra-observer reliability (ICC: 0.92, CI 95%: 0.85 – 0.96) and very good inter-observer agreement (ICC: 0.84, CI 95%:0.72 – 0.91). In conclusion, matching affected and intact contralateral humeral head and glenoid by reconstruction on a computer-based virtual model allows identification of bipolar bone defects and enables quantitative determination of bone loss.