Recent progress in the understanding of the spatial organization of nuclear functions owes a lot to fluorescence in situ hybridization (FISH) methodology. The majority of studies using this technology have been carried out using cultured cells. However, nuclear processes in whole organisms, may be to a notable degree, different from those in cultured cells and actually not similar across different tissues. Therefore, for better understanding of nuclear processes in ex vivo organismal material, it is necessary to study nuclear organization in sections of tissue. FISH on sections is still not common in nuclear biology studies mostly due to methodological problems. The protocol suggested in this chapter is based on several years experience in hybridizing different probes on cryosections of various tissues.