The second Nano-IBCT conference of the COST Action MP1002: Nanoscale Insights into Ion Beam Cancer Therapy was held in Sopot, Poland, from May 20th to May 24th, 2013. The Nano-IBCT action had been launched in December 2010 and brings together experts from different disciplines (physics, chemistry, biology, hadron-therapy centres, medical institutions), with specialisms in the radiation damage of biological matter. This meeting follows up the first one that was held in October, 2011 in Caen, France and we were pleased to see again so many of the participants of the previous meeting as well as to welcome some new colleagues joining and sharing their knowledge and expertise in this field.