High Performance Computing architectures have become incredibly complex and exploiting their full potential is becoming more and more challenging. As a consequence, automatic performance tuning (autotuning) of HPC applications is of growing interest and many research groups around the world are currently involved. Autotuning is still a rapidly evolving research field with many different approaches being taken. This special issue features selected papers presented at the Dagstuhl seminar on “Automatic Application Tuning for HPC Architectures” in October 2013, which brought together researchers from the areas of autotuning and performance analysis in order to exchange ideas and steer future collaborations.