Extraction of nuclei from unmounted archived tissue has become a method widely used for molecular cytogenetic investigations. It is a suitable approach to take advantage of the large series of formalin fixed and subsequently paraffin-embedded material which has been collected in the times before interphase cytogenetic analysis has become possible. We present a new kind of assay for the extraction of nuclei from one single mounted tissue section; the extracted interphase nuclei are suitable very well for a fluorescence in situ hybridization (FISH) approach. The method described has been successfully used for the analysis of the INT2/FGF3-amplicon in 20 samples of oral squamous cell carcinoma.