Tumors and tumor-derived cell lines are typically chromosomally complex and heterogeneous. These features complicate the description of their karyotype. As a first approach to the chromosomal characterization of the two near-triploid thyroid tumor cell lines, BCPAP and FTC 133, the techniques of fluorescence in situ hybridization and comparative genomic hybridization were used and compared. Most of the results obtained by the two methods were in good agreement. The follicular-derived cell line FTC 133 showed more extensive chromosome variation between cells than the papillary-derived cell line BCPAP. Both cell lines had significant gains in part or whole of chromosomes 1, 11, and 20 and losses in chromosomes 16, 21, and 22. BCPAP cells also had gains in chromosomes 4 and 5 and losses in chromosomes 7, 9, and 10; FTC133 cells had gains in chromosomes 6, 7, 8, 14, 15, and 19. Chromosomes 4 and 5 were the most stable in BCPAP cells; in the FTC 133 cells, chromosomes 7 and 19 showed the greatest segregational stability. The results have been discussed in terms of possible karyotype evolution. Moreover, it has been possible to compare the sensitivity limits of the two techniques in the analysis of polyploid tumors. (C) 2002 Elsevier Science Inc. All rights reserved.