Cytokines have validated roles in the immunopathogenesis of inflammatory bowel disease (IBD) with its two major forms ulcerative colitis (UC) and Crohn's disease (CD). The aim of this study was to investigate mRNA expression of proinflammatory IL-23 and IL-17A cytokines, regulatory cytokines IL-10, TGF beta 1, IL-6, and also transcription factor FoxP3 in colonic mucosal samples from IBD and non-IBD-patients. We examined mRNA relative quantities of IL-6, IL-23, and IL-17A, IL-10, TGF beta 1 and FoxP3 genes, in inflamed colonic mucosa samples from 37 patients with IBD and in normal mucosal tissue in 12 persons without IBD by performing relative qRT-PCR assay. All investigated genes, according to RQ value, are upregulated in inflamed mucosa in the following order: IL-6 > FoxP3 > TGFbeta > IL-23 > IL-17A > IL-10. We also observed significant differences between higher gene expression of FoxP3 and IL-6 in inflamed tissue in patients with IBD (p = 0.001, p = 0.000, respectively) compared to normal mucosa of persons without IBD. Moreover, IL-6, TGF beta 1 and FoxP3 were overexpressed more than 10 times (RQ > 10) in inflamed mucosa from IBD patients in comparison with normal mucosa from controls. We also observed significant differences between higher gene expression of FoxP3 and IL-6 in inflamed tissue in patients with UC (p = 0.011, p = 0.000, respectively) and CD (p = 0.008, p = 0.000, respectively), compared to normal mucosa of persons without IBD. We also found an increased TGF beta 1 expression in CD patients alone (p = 0.041). Our results demonstrated significant differences in the expression of mRNA encoded regulatory and effectors cytokines in IBD, compared to healthy control. The obtained specific expression profile, including IL-6 and TGF beta 1 cytokines, simultaneously with the transcription factor FoxP3, may represent a mRNA hallmark for IBD.