In situ hybridization, in situ transcription, and in situ polymerase chain reaction (PCR) are techniques used to detect DNA and RNA sequences within a cell or tissue structure. These three in situ methodologies employ the principles of recombinant DNA to form double-stranded hybrids of DNA-DNA, DNA-RNA, or RNA-RNA. The essence of in situ hybridization (ISH) is the hybridization of a labeled probe to a complementary target sequence, whereas in situ transcription (IST) is the synthesis of complementary DNA incorporating a label directly on the target DNA or RNA within a cell or tissue. In the case of in situ PCR (ISPCR), it is the repeated in situ duplication of both the sense and antisense strands of DNA to increase the number of copies of the target sequence. ISH, IST, and ISPCR each have their advantages and disadvantages. The purpose of this chapter is to address in situ considerations required of these techniques, emphasizing tissue fixation, pre-hybridization steps, DNA probes, RNA probes, oligoprobes, and probe labeling. Five successfully used protocols are presented as examples. Any given nucleotide target sequence may have its own unique set of optimum conditions, thus requiring some adjustment in the hands of the user.