The biological diversity of prostate cancer confounds standardization of therapy. Advances in molecular profiling suggest that differences in the genetic composition of tumors significantly contribute to the complexity of the disease. Alternative pre-mRNA splicing is a key genetic process underlying biological diversity. During alternative splicing, coding and noncoding regions of a single gene are rearranged to generate several messenger RNA transcripts yielding distinct protein isoforms with differing biological functions. Misregulation of the splicing machinery and mutations in key regulatory elements affect splicing of cancer-relevant genes. In prostate cancer, aberrant and alternative splicing generates proteins that influence cell phenotypes and survival of patients. Splicing events may be exploited for clinical benefit, and technological advances are beginning to uncover novel biomarkers and therapeutic targets. Since splicing mediates information transfer from the genome to the proteome, it adds an important dimension to '-omics'-based molecular signatures used to individualize care of patients.