Different lines of evidence suggest that the nuclear matrix (NM), the protein scaffold of the nucleus, represents a functional unit playing a pivotal role in the spatial and temporal coordination of the events of gene activation. Any change in the gene expression pattern, which occurs during carcinogenesis, may partially depend on an impairment of the regulatory functions of the NM. Therefore, increasing interest has been addressed to the study of NM modifications associated with malignant transformations and to potential clinical applications. Here, recent results on the NM changes in prostate cancer are discussed. Tumor cells are characterized by a more complex NM protein pattern compared to normal tissue: the development of poorly-differentiated tumors is characterized by the expression of proteins that are not present in hyperplastic tissues or in more differentiated tumors. In addition, a few newly-expressed proteins are significantly correlated with the risk of biochemical progression. The potential application of these proteins at the diagnostic and prognostic levels calls for further studies.