The fatigue properties of filled elastomers are strongly related to the population of inclusions induced by their complex recipes and mixing/injection processes. The description and the understanding of the basic damage and dissipation mechanisms involved around these inclusions, the influence of their nature, geometry, size, interface and cohesion properties are especially important to optimize the fatigue design of industrial compounds and parts. The objective of the study is to take advantages of tomography observations to characterize the effects of the 3D inclusions on the fatigue resistance of rubber filled with carbon black. An images processing is necessary to dissociate accurately the inclusions of the matrix. The three dimensional observations provide many information on the inclusion's morphology (size, shape) and their spatial distribution. Moreover, the proposed images processing allows detecting cracks inside and on the surface of the specimen, which offers a better insight on the early stages of the fatigue damage scenario. Then, a numerical model and thermo-mechanical measurements are used to understand why some inclusions become initiation sites. Finally, one activated site is fully described as example.