It has been reported that pro-inflammatory cytokines levels like IL-6 and TNF-α can determine the degree of inflammation of ulcerative colitis (UC).To measure the gene expression of IL-6 and TNF-á in patients with UC and controls and to correlate with histological activity.We studied 36 patients with UC, 13 healthy controls and 11 with inflammation. After total ribonucleic acid (RNA) extraction, complementary deoxyribonucleic acid (DNA) was synthesized by polymerase chain reaction (PCR) and relative expression was determined through real-time PCR for IL-6 and TNF-á. Statistical analysis was performed using the Kruskal-Wallis test and Spearman correlation.The expression of IL-6 increases in patients with active UC compared to controls (p = 0.004) as well as UC patients in remission (p = 0.014). There was no significant difference between patients with active UC and controls with inflammation. (p = 0.446). Gene expression of TNF-α was higher in biopsies from patients with UC activity compred with control subjects (p = 0.004), as well as those in remission (p = 0.001). The expression of IL-6 correlated significantly (p = 0.02) with histological activity.The gene expression of IL-6 and TNF-α is increased in active UC. Interleukin 6 is better marker of bowel inflammation because its expression correlates with histological activity.