We are pleased to present the proceedings of the Third Workshop on Algorithms in Bioinformatics (WABI 2003), which took place on September 15-20, 2003 in Budapest, Hungary. The WABI workshop was part of the four-conference meeting, ALGO 2003, which was locally organized by Dr. Jan ' os Csirik, Head of the Department of Computer Science, J' ozsef Attila University, Budapest. See http://www. conferences. hu/ALGO2003/algo_2003. htmfor more details. WABI focuses on discrete algorithms that address important problems in molecular biology, genomics, and genetics, that are founded on sound models, that are computationally e?cient, that have been implemented and tested in simulations and on real datasets, and that provide new biological results. The workshopgoalsareto presentrecentresearchandidentify andexploredirections for future research. We received78 submissionsin responseto the call for papers and 36 were- cepted. We wouldliketo sincerelythank the authorsof allsubmitted papers and the conference participants. We especially thank a terri?c program committee for their diligent and thorough work in reviewing and selecting the papers.