Alternative splicing, defined as the generation of multiple RNA transcript species from a common mRNA precursor, is one of the mechanisms for the diversification and expansion of cellular proteins from a smaller set of genes. Current estimates indicate that at least 60% of genes in the human genome exhibit alternative splicing. Over the past decade, alternative splicing has increasingly been recognized as a major regulatory process with a critical role in normal development. Furthermore, the importance of alternative splicing in disease development and treatment is starting to be appreciated. Therefore, an increasing number of high-throughput genomics and proteomics studies are being performed in order to delineate (a) the changes in alternative splicing under various conditions; (b) the properties and functions of protein isoforms; and (c) the splicing and alternative splicing regulation process. Strategies for the parallel analysis of alternative splice forms by microarray experiments have been conceived, and examples have been published. In addition to the differences in microarray probe design, the analysis of microarrays with probes for exons, exon/exon junctions as well as specific splice forms is significantly different from the standard experiment. Several methods are being developed in order to address the particular needs of alternative splicing microarrays. Many reviews have already dealt with alternative splicing. However, high-throughput analysis methods that are becoming increasingly popular have not received much attention. Here, we will provide an overview of the tools and analysis methods that were developed specifically for alternative splicing microarrays described in terms of specific experiments.