The perinucleolar compartment (PNC) is a dynamic, irregularly shaped, and electron-dense nuclear structure that is physically associated with the nucleolus (1). It is found predominantly in transformed cells and various cancer tissues, and rarely in normal cells (1). The components of the PNC described to date include several small RNAs transcribed by RNA polymerase (pol) III, and several RNA binding proteins of which some are primarily implicated in pre-messenger RNA (mRNA) processing (2). The current working model suggests that the PNC is a dynamic functional organelle involved in the metabolism and trafficking of a subset of newly synthesized pol III RNAs in transformed cells. The PNC can be localized and visualized in tissue sections by a immunohistochemical technique using the mouse monoclonal antibody SH54 (3), which specifically recognizes the RNA binding protein PTB (polypyrimidine tract binding protein), which is highly concentrated in the PNC and is used as a marker for PNC detection. The prevalence of PNCs has been found to be correlated with disease progression in breast cancer (3) and in tumors from other tissues, including prostate, colon, ovary, and endometrium (our unpublished studies). PNC prevalence increases with the degree of malignancy and reaches nearly 100% in distant metastases. A high PNC prevalence is associated with poor prognosis (our unpublished studies) (3). In this chapter, we describe methods, which are still under development, for PNC detection and PNC prevalence scoring. Due to the intrinsic limitations of immunocytochemistry using peroxidase assays, the signal intensity can vary from experiment to experiment. Studies are underway to optimize an automated protocol to increase its reproducibility and accuracy.