Microsatellite instability (MSI) and loss of heterozygosity (LOH) in chromosomes 9 and 16 have been reported in human breast cancers. In order to determine whether changes in these chromosomes play a role in the initiation and progression of this disease, we performed microsatellite polymorphism analyses in human breast epithelial cells (HBEC) transformed by chemical carcinogens, an in vitro system that recapitulates various stages of neoplastic transformation. In this experimental system we studied the mortal HBEC MCF-10M, immortal MCF-10F cells, derived from MCF-10M cells, and clones derived from MCF-10F cells treated with benzo[a]pyrene (B[a]P) (BP1 and BP1E) and 7,12-dimethylbenz[a]anthracene (DMBA) (D3 and D3-1). The four clones of transformed cells were injected into severe combined immunodeficient (SCID) mice. Only BP1-E cells induced the formation of tumors, designated BP1E-Tp cells. These cells originated six additional tumors, designated BP1E-Tf no. 1 through Tf no. 6. Microsatellite analyses were carried out using five markers for chromosome 9 and 20 for chromosome 16. There was no evidence of MSI or LOH in clones BP1 and BP1E when compared with the MCF-10M and MCF-10F cells, whereas BP1E-Tp cells and Bp1E-Tf no. 1-Tf no. 6 tumors exhibited MSI at loci p23 and p21, and LOH at p21-22 of chromosome 9. They also exhibited MSI and LOH at multiple loci of both the short and long arms of chromosome 16, i.e. p13.13, p13.3, p12, q12.1, q12.2, q23 and q24, to which putative tumor suppressor genes have been localized. Clones D3 and D3-1 exhibited no genomic changes in chromosome 9, but did show MSI at locus q12.1 of chromosome 16 using marker D16S285. Although the cells treated with DMBA expressed early phenotypes of neoplastic transformation, they were not tumorigenic, and also manifested fewer changes than the tumorigenic BP1E-Tp cells and the tumors BP1E-Tf. The changes in chromosomes 9 and 16 observed in these latter ones indicated an association with the expression of tumorigenesis, which represents a late event in the progression of the neoplastic transformation of HBEC. Of interest was the observation that HBEC transformed by chemical carcinogens in vitro express genomic changes similar to those found in spontaneous breast carcinomas.