We have developed a program, GENECUT, for analyzing datasets from gene expression profiling. GENECUT is based on a pairwise clustering method known as Normalized Cul [Shi and Malik, 1997]. GENECUT extracts global structures by progressively partitioning datasets into well-balanced groups, performing an intuitive k-way partitioning at each stage in contrast to commonly used 2-way partitioning schemes. By making use of the Nystrom approximation, it is possible to perform clustering on very large genomic datasets.