Protein patterns in six samples from primary vaginal cancers, in five from normal vaginal tissue and in five primary cervical cancers, were analysed using two-dimensional polyacrylamide gel electrophoresis (2-DE). Protein expression profile was evaluated by computer-assisted image analysis (PDQUEST) and proteins were subsequently identified using matrix-assisted laser desorption/ ionisation mass spectrometry. The aim was to analyse the protein expression profiles using the hierarchical clustering method in vaginal carcinoma and to compare them with the protein pattern in cervical carcinoma in order to find a helpful tool for correct classification and for increased biomedical knowledge. Protein expression data of a distinct set of 33 protein spots were differentially expressed. These differences were statistically significant (Mann -Whitney signed-Ranked Test, Po0.05) between normal tissue, vaginal and cervical cancer. Furthermore, protein profiles of pairs of primary vaginal and cervical cancers were found to be very similar. Some of the protein spots that have so far been identified include Tropomyosin 1, cytokeratin 5, 15 and 17, Apolipoprotein A1, Annexin V, Glutathione-S-transferase. Others are the stress-related proteins, calreticulin, HSP 27 and HSP 70. We conclude that cluster analysis of proteomics data allows accurate discrimination between normal vaginal mucosa, primary vaginal and primary cervical cancer. However, vaginal and cervical carcinomas also appear to be relatively homogeneous in their gene expression, indicating similar carcinogenic pathways. There might, further, be a possibility to identify tumour-specific markers among the proteins that are differentially expressed. The results from this study have to be confirmed by more comprehensive studies in the future. Primary carcinoma of the vagina (PCV) is a rare disease affecting predominantly postmenopausal women (Pecorelli, 2001). Histologically, the majority of PCV consist of squamous cell carcinomas (Pecorelli, 2001). Owing to the rarity of this disease, little is known about the aetiological and prognostic factors. Like cervical carcinomas, PCV has been shown to be associated with HPV, but only in about 50% of the cases (Daling and Sherman, 1992;Hildesheim et al (1997)). The prognosis for PCV is quite poor with an overall 5-year survival rate of about 50%, which is worse than for cervical carcinoma (Pecorelli, 2001). Early detection is crucial for the prognosis.It has been suggested that vaginal and cervical carcinomas have common aetiology since vaginal tumours often occur as second primary malignancy in patients with a history of cervical dysplasia and/or neoplasia or hysterectomy due to these disorders (Choo and Anderson, 1982;Benedet et al, 1983;Brinton et al, 1990;Eddy et al, 1991;Kirkbride et al, 1995). In the clinical situation, it is sometimes difficult to discriminate between cervical and vaginal carcinomas, especially in patients with prior cervical disease. As 95% of the recurrences of cervical carcinoma occur within 5 years, ma...