Cytokine polymorphisms may influence both the risk of developing oral lichen planus (OLP) and the outcome of hepatitis C virus (HCV)-infected patients and OLP has been frequently associated with HCV infection. The aim of the present study was to analyse whether cytokine polymorphisms may influence the susceptibility to HCV-related OLP. Thirty-five patients with OLP and chronic HCV infection (OLP-HCV+ve) took part in the study. As controls, 44 patients with OLP but without HCV (OLP-HCV-ve) infection and 140 healthy donors were studied. Thirteen cytokine genes with 22 single nucleotide polymorphisms (SNP) were studied. IFN-gamma UTR 5644 genotype frequencies showed an increase in number of A/T heterozygote in OLP-HCV+ve patients compared with OLP-HCV-ve that approached the statistical significance [P = 0.03, P-corrected (PC) = 0.66]. Contrarily, in OLP-HCV+ve patients, the frequency of genotype -308 G/A of the TNF-alpha was decreased, whereas the genotype -308 G/G was increased compared with OLP-HCV-ve (P = 0.0005, PC = 0.011 and P = 0.0016, PC = 0.0352, respectively). OLP patients with and without HCV infection showed a different genetic cytokine background suggesting distinct pathogenetic mechanisms.