The availability of sensitive methods for detecting and localising the feline immunodeficiency virus (FIV) may help shed light on its role in generating tissue damage observed during infection. As immunohistochemical and in situ hybridisation techniques might not be sufficiently sensitive for this type of study, we adapted to FIV PCR-in situ hybridisation (PCR-ISH) that combine the extreme sensitivity of PCR with the precise localisation provided by ISH. The steps important for the success of PCR-ISH, such as sample preparation, permeabilisation, amplification profile, type of labels, and hybridisation conditions were optimised using paraformaldehyde-fixed and formalin-fixed paraffin-embedded sections of cells infected in vitro with FIV. As controls for amplification, the feline tumor necrosis factor-alpha gene (TNF-alpha) and the non-related EBNA-1 gene of the human Epstein-Barr virus were used. Once the method proved sufficiently sensitive and specific with these cells, the PCR-ISH assay was applied to paraffin sections of the lymph nodes, spleen and central nervous system of a 2-year FIV infected cat that, at the time of challenge, harboured low copy numbers of proviral genomes. Comparison of the results of PCR-ISH, competitive PCR and immunohistochemical analysis are described.