This book constitutes the refereed proceedings of the 5th International Workshop on Experimental and Efficient Algorithms, WEA 2006, held in Menorca, Spain, May 2006. The book presents 26 revised full papers together with 3 invited talks. The application areas addressed include most fields applying advanced algorithmic techniques, such as combinatorial optimization, approximation, graph theory, discrete mathematics, scheduling, searching, sorting, string matching, coding, networking, and more.