The evaluation of gene expression in the context of cellular morphology is essential to the full understanding of cell biology. A variety of methods for detection of nucleic acids are currently available. Solution PCR requires disruption of the sample and detection of the amplified material by electrophoresis in agarose gels. In situ Hybridization methods, on the other hand, permit morphological correlation and provide a high sensitivity that is sufficient for many applications. In some instances, however, the amount of target in the sample is below the limit of detection of this technique. In situ PCR allows the detection of minimal amounts of nucleic acids with exquisite sensitivity and specificity, while the integrity of the cells and the morphology of tissues remains preserved. This technique, although not exempt from difficulties, is undergoing methodological simplifications that will make it suitable for an increasing number of basic science and clinical applications. The following is a review of the principles, methods and applications of In situ PCR.