The 4th IAEA technical meeting (TM) on the Theory of Plasma Instabilities was held in Kyoto, May 18th--20th 2009, following the first (Seeon), second (Trieste) and third (York) meetings in this series. This IAEA-TM was motivated by the recent advances in theoretical methodology, the rapid progress in observations of laboratory and astrophysical plasmas and the evolution of fusion research as we approach the ITER era. The international advisory committee (IAC) and local organizing committee (LOC), the members of which are listed below, collaborated to define the scope and the content of the scientific programme.Young scientists were actively encouraged to participate in this TM to help stimulate their future research careers and raise their international profiles. Through these young scientists, the IAEA-TM planned to identify the future directions of research. About 90 researchers, from 13 countries and the IAEA, participated in this IAEA-TM, with 72 scientific presentations. The talks and posters generated enthusiastic discussions, contributing to the vibrancy of the meeting.This special issue of Nuclear Fusion consists of a cluster of papers, reporting some of the main contributions to the IAEA-TM. The articles in this cluster are representative of the scientific width of presentations at the meeting, spanning topics from micro-turbulence to large-scale MHD dynamics and from transport to detailed analysis of diagnostics. They demonstrate the quality and depth of the research presented at the conference.List of IAC (alphabetical order):B. Breizman (USA), S. Guenter (Germany), T. S. Hahm (USA), K. Itoh (Japan, Chair of 2009), Ya. I. Kolesnichenko (Ukraine), A. G. Peeters (UK), H. Wilson (UK)List of LOC (alphabetical order):A. Fukuyama, R. Horiuchi, S.-I. Itoh, N. Kasuya, Y. Kishimoto (co-chair), K. Kusano, J. Li, K. Mima, S. Murakami, H. Naitou, N. Nakajima, Y. Nakamura, H. Ohtani, S. Okamura, T. Ozeki, S. Sudo (co-chair), H. Sugama, Y. Todo, S. Tokuda, S. Usami, M. Yagi, Z. Yoshida