This volume contains the proceedings of the 7th Conference on Computational Methods in Systems Biology (CMSB 2009), held in Bologna, from August 31 to September 1, 2009. The first CMSB was held in Trento in 2003, bringing together life scientists, computer scientists, engineers and physicists. The goal was to promote the c- vergence of different disciplines aiming at a new understanding and description of biological systems, firmly ground in formal models, supported by compu- tionallanguagesandtools,andofferingnew methodsofanalysis.The conference then moved to Paris in 2004, Edinburgh in 2005, Trento in 2006, Edinburgh in 2007 and Rosk/Warnemunde ¨ in 2008. This year the conference attracted about 45 submissions form 18 countries, mainly from Europe and North America, but also from Asia and Australia. We wish to thank all authors for their interest in CMSB 2009. After careful disc- sions, the Programme Committee eventually selected 18 papers for presentation at the conference. Each of them was accurately refereed by at least three - viewers, who delivered detailed and insightful comments and suggestions. The Conference Chairmen warmly thank all the members of the Programme C- mittee and all their sub-referees for the excellent support they gave, as well as for the friendly and constructive discussions. We also would like to thank the authorsfor havingrevisedtheir papers to addressthe comments andsuggestions by the referees.