Systems medicine research studied health and diseases through the investigation of several layers of knowledge (biological, psychological, social and environmental, the so called “Omics”) and could be interpreted as an informational science in which the interpretation of a multilayer analysis could analyze the dynamic of the pathological process over time. New technologies for large-scale data analysis and a definition of a multidimensional minimal data set for everyone are under investigation to override a simple mechanistic interpretation. For these reasons “Omics” are part of the dynamic study of allogeneic transplanted patients and should be integrated with the interpretation of the connections between individual and family, society, environment and health system. This process is crucial for the personalization of the transplanted patient's care. The interaction of the several inter- and intra-individual layers over time will contribute to a new sets of complex phenotypes typical for the transplanted patient. In a few years, billions of data concerning complex phenotypes will be available for everyone. Personalization, prevention, prediction and participation are thus cornerstones of the care for such complex patients and Information Technologies will be part of this research process.