With the maturation of the technology for fabricating and scanning high-density gene expression microarrays, information processing issues loom over as the fundamental challenge to the widespread use of this technology. These issues can be broadly organised into three interrelated categories: data tracking and management, image analysis and expression level quantification, and data mining and analysis. Data tracking and management requires tools for automated tracking of samples and generation of mapping tables to specify what has been spotted at each location on a microarray slide. The image processing issues are one of the more important and difficult issues at this time. Issues with proper image segmentation, separating signal from background and contamination, must be effectively dealt with in an automated fashion. A number of sophisticated approaches have been developed and will be presented. The data analysis and mining issues require a uniform and flexible method of data representation and normalisation to allow for sharing of data among different “data suppliers”. Once the data is made available a number of clustering and dimensionality reduction approaches can be used to analyse, visualise and compare various experiments together. We will describe software tools for performing these operations.