Polymorphisms of the proinflammatory and immunoregulatory cytokines, tumor necrosis factor-alpha (TNF-alpha) and lymphotoxin-alpha (LTA), have been shown to affect their production and be associated with Crohn's disease. However, the actual alleles associated with the disease are variable among populations. The aim of this study was to test whether TNF-alpha and LTA polymorphisms were associated with Crohn's disease risk in Korean samples. Genotyping for five TNF-alpha promoter polymorphisms (-1031, -863, -857, -308, and -238) and two LTA polymorphisms (intron 1 and Thr60Asn) were performed on 289 Korean patients with Crohn's disease and 399 unrelated healthy controls. Carriers of an individual polymorphism of TNF-alpha at -857T, showed statistically significant association with Crohn's disease (adjusted OR=1.64, 95% CI=1.11-2.41, P=0.013). Following haplotype analysis, carriers of the haplotype consisted of the -1031C, -863A, and -857C alleles showed statistically significant association with Crohn's disease (adjusted OR=1.54, 95% CI=1.02-2.32, P=0.040). Significantly reduced frequencies were seen for the carriers of the LTA Thr60Asn polymorphism in patients (OR=0.62; 95% CI=0.42-0.93, P=0.019), suggesting a protective effect on Crohn's disease. Our data support the hypothesis that the TNF-alpha/LTA genotypes play an important role in the pathogenesis of Crohn's disease in Koreans.