OBJECTIVE: The purpose of the study was to investigate benign and malignant squamous cervical cells obtained by cervical swabs with regard to differentially expressed genes and gene expression profiling, in order to evaluate the biological behavior and clinical outcome of cervical malignancies. METHODS: Cervical squamous cells from six women with high-risk human papillomavirus positive [HR-HPV(+)] cervical carcinoma and from six HPV-negative women with normal ectocervical cells were analyzed by cDNA array. RESULTS: cDNA over-expression of several genes such as MET (c-met), Nm23-H1 (NME1), EGFR, KGFR, Nm23-H2 (NME2), ERBB2 (c-erbB-2), cyclin-dependent kinase inhibitor 4 (CDKN2A, p16INK4A), cytokeratin 8 (KRT8), KRAS (K-ras), FLT1, KGF (FGF7), BCL2-like 2 protein (BCL2L2), ERBB4, MYCN (N-myc), cyclin D1 (CCND1), KIT (c-kit), secreted phosphoprotein 1 (SPP1) and STAT1, was significant in cervical squamous cell carcinoma (CSCC). Gene expression was downregulated for 13 genes in CSCC, such as interleukin 1 alpha (IL1A), the transforming growth factor receptor beta superfamily (TGFbeta; TGFB), some members of the insulin-like growth factor binding proteins (IGFBPs) and the integrin family (ITGA6, ITGB1). CONCLUSION: This study was focused on the gene expression profiling of HR-HPV(-) and (+) cervical squamous cells and CSCC obtained by cytobrush. We observed gene expression patterns and signaling pathways that permit the investigator to distinguish between benign squamous cervical cells and CSCC with and without HPV infection.