Biomedical engineering and medical informatics represent challenging and rapidly growing areas. Applications of information technology in these areas are of paramount importance. Building on the success of the first ITBAM that was held in 2010, the aim of the second ITBAM conference was to continue bringing together scientists, researchers and practitioners from different disciplines, namely, from mathematics, computer science, bioinformatics, biomedical engineering, medicine, biology, and different fields of life sciences, so they can present and discuss their research results in bioinformatics and medical informatics. We trust that ITBAM served as a platform for fruitful discussions between all attendees, where participants could exchange their recent results, identify future directions and challenges,.