Although flow cytometric DNA ploidy has turned out as a significant predictor of survival in oral squamous cell carcinoma, little is known about the underlying karyotypic structure of gross aneuploidy. We therefore analysed one diploid and 9 aneuploid carcinomas with relative DNA contents between 1.1 and 2.8 by fluorescence in situ hybridization with topologic markers for the centromere (3cen) and the terminal regions (3p, 3q) of chromosome 3. Progressing deviation of aberrant DNA contents from the normal diploid value correlated with increasing 3cen copy numbers per cell. A pronounced marker heterogeneity suggested that DNA-aneuploid cell populations consisted of karyotypically different clones. Monosomy of 3p was the only chromosomal alteration in the DNA diploid tumour. A significant 3p underrepresentation was a recurrent finding also in 7 of 9 aneuploid carcinomas while a subset of cells in each of 2 other cases showed a complete loss of one sister chromosome 3. In contrast, 7 of 9 aneuploid tumours exposed corresponding 3q and 3cen copy numbers, 2 showed a substantial 3q overrepresentation. It appears that amplification of chromosome 3 plays a role in the development of aneuploidy and the concurrent overexpression of 3q target genes. Acquired loss of the short arm of chromosome 3 in DNA-diploid tumour cells may contribute to the manifestation of recurrent 3q deletions in aneuploid cell populations.

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