In addition to exogenous risk factors, the development of head and neck cancer is based on genetic alterations and individual sensitivity to mutagens. The DNA-damaging effect of xenobiotics and the location of chromosomal changes warrant further investigation. The aim of this study was to evaluate variance in structural genetic changes in human epithelia as target cells for head and neck carcinogenesis. The combination of the single-cell gel electrophoresis (Comet) assay with the fluorescence in situ hybridization (FISH) technique is presented to examine differences in sensitivity to DNA-damage induction and in alterations of chromosomes 1, 3, 5 and 8 in patients with and without squamous cell carcinoma of the oropharynx. Macroscopically healthy biopsies from the mucosa, taken at a distance from the tumor of 10 patients with oropharyngeal carcinoma and from 10 patients without tumor were harvested during surgery. Cells were isolated by enzymatic digestion and incubated with benzo[a]pyrene-diolepoxide (BPDE), causing DNA-adduct formation by covalent binding of BPDE with DNA bases. The cells were subsequently analyzed by means of the Comet assay to separate DNA fragments and to visualize the DNA-damage. A hybridization mixture with whole-chromosome paints for Chr1, Chr3, Chr5 and Chr8 was added. After fluorescent staining, the entire DNA and the DNA of chromosomes 1, 3, 5 and 8 were evaluated by digital analysis. BPDE caused significant DNA damage in oropharyngeal mucosa cells of patients with and patients without carcinoma. No differences in the amount of DNA damage could be observed between patients suffering from sqamous cell carcinoma and patients without malignancy. Evaluation of chromosomal alterations, however, revealed significantly higher damage levels in chromosomes 3, 5 and 8 compared with chromosome 1 in tumor patients. In contrast, for patients without oropharyngeal carcinoma no differences in chromosomal alterations could be observed. The Comet assay could be combined with FISH to examine the sensitivity to DNA-damage induction and chromosomal alterations in human epithelial cells exposed to a genotoxic agent. Chromosomal breakage is increased for chromosomes 3, 5 and 8 as compared with chromosome 1, indicating a higher sensitivity of these chromosomes in epithelial cells of tumor patients. Using Comet/FISH on human epithelia, selected genetic alterations can be detected, which supports description of endogenous risk factors in carcinogenesis of the upper aerodigestive tract.