Abstract Genomic instability is one of the main characteristics of malignant tumors, including HPV‐induced cervical cancer. The aim of this study was to explore the use of assessing chromosome aberrations (CA) in peripheral blood lymphocytes as a biomarker for genomic instability in high‐risk HPV‐infected women with high‐grade squamous intraepithelial lesions (HGSIL). A total of 120 women were recruited for this study, following cytology/colposcopy evaluation and HPV DNA detection. The study groups consisted of 30 HPV(+) women with histologically confirmed cervical intraepithelial neoplasia grade 2/3 and 30 HPV(+) women with carcinoma in situ (CIS). Two control groups, including 30 women HPV(−) and 30 women HPV(+), were recruited among women who were reported as cytology negative. Lymphocyte cell cultures were established for 52 hr, and 100 complete metaphase cells were evaluated per subject for CA analysis. The results show that women with CIS had significantly higher frequencies of both aneuploidy (0.67 ± 0.20 vs. 0.14 ± 0.08, P = 0.020) and tetraploidy (0.88 ± 0.23 vs. 0.17 ± 0.08, P = 0.013) in comparison with HPV(−) controls. These findings suggest the usefulness of peripheral blood lymphocytes to detect genomic instability associated with HPV‐induced HGSIL. Environ. Mol. Mutagen., 2008. © 2008 Wiley‐Liss, Inc.