Systems biology and bioinformatics are widely recognized as the fields of biological science that have been developed very rapidly in this century. In these fields, there is a much-needed development of computational tools to deal with a monumental amount of genomic and post-genomic data, aiming at systems-level understanding in biology. The Third International Conference on Computational Systems-Biology and Bioinformatics (CSBio 2012) was organized to provide scientists and researchers in the area of computational systems biology and bioinformatics with a forum to share and exchange their knowledge and experiences. Besides, CSBio 2012 was the venue for all participants to survey the current status of development of research works on the application of computational systems biology and bioinformatics in the biotechnological fields: agriculture, energy and environment, as well as medicine. CSBio 2012 was co-organized by King Mongkut's University of Technology, Thonburi (KMUTT) and the National Center of Genetic Engineering and Biotechnology (BIOTEC), and it was held on October 3-5, 2012, at the Centara Grand, Central Plaza Ladprao, Bangkok, Thailand.