Treatment of common pathologies of the shoulder complex, such as rheumatoid arthritis and osteoporosis, is usually performed by total shoulder arthroplasty (TSA). Survival of the glenoid component is still a problem in TSA, whereas the humeral component is rarely subject to failure. To set up a finite element analysis (FEA) for simulation of a TSA in order to gain insight into the mechanical behaviour of a glenoid implant, the modelling procedure and the application of boundary conditions are of major importance because the computed result strongly depends upon the accuracy and sense of realism of the model. The goal of this study was to show the influence on glenoid stress distribution of a patient-specific bone density distribution compared with a homogenous bone density distribution for the purpose of generating a valid model in future FEA studies of the shoulder complex. Detailed information on the integration of bone density properties using existing numerical models as well as the applied boundary conditions is provided. A novel approach involving statistical analysis of values derived from an FEA is demonstrated using a cumulative distribution function. The results show well the mechanically superior behaviour of a realistic bone density distribution and therefore emphasise the necessity for patient-specific simulations in biomechanical and medical simulations.