The aim of the present study was to determine the relevant major histocompatibility complex (MHC) class II alleles in the genetic susceptibility to systemic lupus erythematosus (SLE) in Mexican Mestizo patients. We examined the gene and haplotype frequencies of the HLA-DRB1, DQA1 and DQB1 alleles by polymerase chain reaction-sequence-specific oligonucleotide probes in 81 Mexican SLE Mestizo patients and 99 ethnically matched controls. We found a significantly increased frequency of the HLA-DRB1*0301 (p(c) = 0.031, odds ratio = 2.63) allele and significantly decreased frequencies of the DRB1*0802 (p(c) = 0.035) and DRB1*1101 (p(c) = 0.037) alleles in the SLE group. Haplotype analysis showed increased frequencies of DRB1*0301-DQA1*0501-DQB1*0201 (p(c) = 0.017, odds ratio = 2.97), and decreased frequency of DRB1*0802-DQA1*0401-DQB1*0402 (p(c) = 0.034) in SLE patients. The most frequently detected haplotypes in SLE patients showed different haplotypic combinations in the homologous chromosome from those found in controls. Thus, the combinations detected in SLE patients were either not detected in the control group or infrequently found. The results suggest that the DRB1*0301 is the principal class II allele associated with the genetic susceptibility to SLE in Mexican patients and that the presence of a specific haplotype of the homologous chromosome in patients with DRB1*0407-DQA1*03-DQB1*0302 and DRB1*1501-DQA1*0102-DQB1*0602 haplotypes could have an additive effect on the susceptibility to the disease. Finally, the low frequency of the DRB1*0301 and DRB1*1501 alleles in the control population suggests that the genetic admixture between Mexican Indians and Caucasian populations was an event that could have increased the risk of Mexicans to develop SLE.