This book constitutes the refereed proceedings of the 5th International Symposium on Stochastic Algorithms, Foundations and Applications, SAGA 2009, held in Sapporo, Japan, in October 2009. The 15 revised full papers presented together with 2 invited papers were carefully reviewed and selected from 22 submissions. The papers are organized in topical sections on learning, graphs, testing, optimization and caching, as well as stochastic algorithms in bioinformatics.