The importance of alternative RNA splicing in the generation of genetic diversity is now widely accepted. This article highlights how alternative RNA splicing can have an impact on drug efficacy and safety, and demonstrates its potential pharmacogenomic value. The analysis of the repertoire of alternative RNA splicing events could potentially identify markers of pharmacogenomic relevance with high sensitivity and specificity and also provides a route through which genes can be selected for single nucleotide polymorphism (SNP) genotyping. Recent methodological advances, including microarray and splice-dedicated expression profiling, have made it possible to perform high-throughput alternative splicing analyses.