In spite of advancement in biomaterials and biomechanics, in development of new osteo-integrative materials and coatings, and in macro- micro- component design, a non negligible fraction of the implanted prosthesis fails before the expected lifetime. A prospective observational clinical study has been conducted to define and apply a set of experimental techniques to in-deep assess the failure of joint prosthesis. Microbiological, histological and micro-structural techniques were implemented to specifically address phenomena occurring at the tissue-implant interface. Results obtained from 27 cases of prosthetic joint failure are discussed in terms of sensitivity and specificity. A procedural flow-chart is finally proposed for the assessment of joint prosthesis failure.