The ISMB2001 conference provides a general forum for dissemi- nating the latest developments in bioinformatics. It is the 9th conference in a truly multidisciplinary conference series that brings together scientists from computer science, molecular biology, mathematics and statistics. Its scope includes the deve- lopment and application of advanced computational methods for biological problems. Relevant computational techniques include, but are not limited to: Machine learning, pattern recognition, knowledge representation, databases, combinatorics, stochastic modelling, string and graph algorithms, linguistic methods, robotics, constraint satisfaction, and parallel computation. Biological areas of interest include biomolecular structure, genomics, biomolecular sequence analysis, evolution and phylogene- tics, biomolecular interactions, metabolic pathways, regulatory networks, developmental control, and molecular biology generally. Emphasis is placed on the validation of methods using real data sets, on practical applications in the biological sciences, and on development of novel computational techniques.