The Second International Conference on High-Performance Computing and Appli- tions (HPCA 2009) was a follow-up event of the successful HPCA 2004. It was held in Shanghai, a beautiful, active, and modern city in China, August 10-12, 2009. It served as a forum to present current work by researchers and software developers from around the world as well as to highlight activities in the high-performance c- puting area. It aimed to bring together research scientists, application pioneers, and software developers to discuss problems and solutions and to identify new issues in this area. This conference emphasized the development and study of novel approaches for high-performance computing, the design and analysis of high-performance - merical algorithms, and their scientific, engineering, and industrial applications. It offered the conference participants a great opportunity to exchange the latest research results, heighten international collaboration, and discuss future research ideas in HPCA. In addition to 24 invited presentations, the conference received over 300 contr- uted submissions from over ten countries and regions worldwide, about 70 of which were accepted for presentation at HPCA 2009. The conference proceedings contain some of the invited presentations and contributed submissions, and cover such research areas of interest as numerical algorithms and solutions, high-performance and grid c- puting, novel approaches to high-performance computing, massive data storage and processing, hardware acceleration, and their wide applications.