Tumor necrosis factor alpha (TNF-alpha) gene is located within the class III region of the major histocompatibility complex (MHC) on the short arm of the human sixth chromosome. Two polymorphisms in the promoter region of the TNF-alpha gene (-308 and -238) have been associated with the genetic susceptibility to develop ulcerative colitis in both Caucasian and Asian populations. The aim of this study was to determine the role of TNF-alpha gene polymorphisms and those from the HLA-DRB1 locus in the susceptibility to develop ulcerative colitis (UC). Eighty Mexican mestizo patients suffering from UC and 99 ethnically matched unrelated healthy controls were genotyped for two TNF-alpha polymorphisms located in the promoter region (positions -308, -238) by polymerase chain reaction (PCR) and amplification refractory mutation system (ARMS) as well as high resolution DNA typing for HLA-DRB1 alleles were performed. The frequency of individuals positive for allele 2 of the TNF(-308) polymorphism was significantly higher in UC patients than healthy controls (23.7% versus 3%, pC = 0.00002; OR = 10.1; CI 95% = 2.69-26.8). No statistically significant deviation from normality was found between TNF*A (-238) and UC Mexican patients. Clinical manifestations such as pancolitis, extraintestinal manifestations and colectomy were not associated with any of the TNF promoter region polymorphisms. However, HLA-DRB1*15 was found to be associated with pancolitis and HLA-DRB1*0103 with the need of proctocolectomy. In conclusion, this clinical differential pattern of association distinguished in two neighboring loci within the MHC region suggest an independent role of the TNF locus in the genetic susceptibility to develop UC.