Although the idea of the personalization of patient care dates back to the time of Hippocrates, recent advances in diagnostic medical imaging and molecular medicine are gradually transforming healthcare services, by offering information and diagnostic tools enabling individualized patient management. Facilitating personalized / precision medicine requires taking into account multiple heterogenous parameters, such as sociodemographics, gene variability, environmental and lifestyle factors. Therefore, one of the most critical challenges in personalized medicine is the need to transform large, multi-modal data into decision support tools, capable of bridging the translational gap to the clinical setting. Towards these challenges, deep learning (DL) provides a novel approach, which enables obtaining or developing high-accuracy, multi-modal predictive models, that allow the implementation of the personalized medicine vision in the near future. DL is a highly effective strategy in addressing these challenges, with DL-based models leading to unprecedented results, matching or even improving state-of-the-art prediction/detection rates based on both intuitive and non-intuitive disease descriptors. These results hold promise for significant socio-economic benefits from the application of DL personalized medicine.