Epulus is a benign gingival tumour of unknown aetiopathogenesis. Classification is inconsistent, and standard management strategies are lacking. Epuli are generally believed to be inflammatory rather than neoplastic lesions. The literature does not present any molecular analysis of the tumour characteristics. The purpose of the present study was to compare benign (epulus) and malignant (cancer) gingival hyper-plasias with regard to the activity of the genes of apoptosis, proliferation, and inflammation using RT-PCR. The investigation involved 70 patients with epuli and 15 patients with gingival squamous cell carcinoma. Each subject had specimens collected from the tumour, tissue margin (incision line), and healthy tissue. Molecular investigations by RT-PCR were used to evaluate expression levels of the genes associated with apoptosis (Bcl-2, Bax, Bcl-2/Bax), proliferation (H3 histone), and inflammatory processes (IFN-gamma, IFN gamma-R1, IFN-gamma R2, IFN-gamma R1/IFN-gamma R2). Correlations have been disclosed between apoptosis and proliferation genes expression in giant cell epuli and high-differentiated gingival squamous cell carcinoma. In RT-PCR molecular analysis, giant cell epulus shows characteristics of a neoplastic lesion, while other epulus types seem to be inflammatory tumours.