The detection of genetic abnormalities in paraffin sections by fluorescence in situ hybridization (FISH) is widely used in clinical practice to detect amplification of the ERB2 gene in breast carcinoma and various chromosomal translocations in lymphomas and soft tissue tumors. However, interpretation of FISH signals in tissue sections may be difficult due to overlapping nuclei and nuclear truncation artifacts. Some of these shortcomings may be avoided by the use of isolated nuclear preparations. However, identification of cell populations may be difficult in detached cells removed from their histological context. We have described an optimized immunoFISH technique on isolated nuclear suspension, which combines the benefits of studying isolated cells derived from paraffin embedded tissues by FISH analysis with the ability to detect cell lineage and other markers by immunofluorescence.