Targeted therapy of proteasome regulated gene expression has potential utility in cancer treatment since components of ubiquitin-mediated proteolysis are altered in human malignancy. Specific regulators of proteasome degradation such as F-box proteins of the SCF E3 ligase complex are ideal biomarkers for assessing therapeutic efficacy since these components determine substrate specificity. An F-box protein that appears to be important in this process is human Cdc4 (Fbw7) since expression is detected in a variety of human cancers including breast, colon, pancreas and uterus. The role of Cdc4 in tumorigenesis appears to be related at least in part to regulation of cyclin E since inactivating mutations of CDC4 in cancer cells leads to cyclin E overexpression and genomic instability. In order to investigate the potential biological and clinical consequences of proteasome inhibition with respect to Cdc4 mediated targeted proteolysis, we investigated CDC4 expression and genetic alterations in 53 primary human prostate cancers in addition to correlation with relevant histopathological and clinical parameters. We identified genetic alterations in 6% of our prostate cancers while differential expression of Cdc4 isoforms correlated with advanced pathological stage and clinical recurrence. Our data suggest that CDC4 expression in prostate cancer has important biological and clinical implications since genetic alterations, differential Cdc4 isoform expression, histopathological and clinical correlation were demonstrated in our analysis. Therefore molecular genetic analysis of CDC4 expression may be an important biomarker for concurrent or subsequent clinical investigation of proteasome targeted therapy in men with prostate cancer.