Recent years have seen an explosion in the techniques available for detailed analysis of histopathological samples allowing improvements to be made in terms of both accuracy of diagnosis and, in certain instances, providing important prognostic information. The two broad areas where most interest has focused are in the investigation of cellular proteins/protein products by immunohistochemistry and the analysis of genes and transcripts using a range of molecular techniques. The numbers of reagents available for immunohistochemical applications in veterinary species are steadily increasing although still lag significantly behind the human diagnostic field in this respect. Molecular techniques currently in use include the polymerase chain reaction (PCR) and in situ hybridisation (ISH). More recent advances in terms of molecular analysis include the techniques of microarray, laser capture microdissection and proteomics which allow analysis of the genetic and protein repertoire of individual cell populations. This technology is extremely powerful with the potential to provide vast amounts of data. This review focuses on these techniques as they apply to the detailed analysis of tumours.