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Introduction: Systemic lupus erythematosus is an autoimmune disease with higher prevalence in women. Single nucleotide variants in genes involved in the regulation of autoreactive cells, such as PTPN22 rs2488457C˃G, and TRAF1-C5 rs10818488A˃G and rs3761847G˃A, have been associated with the disease in some populations; however, little is known about these variants in the Mexican mestizo population. Aim: We analyzed whether these variants are associated with lupus in women from Central Mexico and Yucatan. Methods: DNA samples from two hundred female patients with lupus (100 from Yucatan and 100 from Central Mexico) and 200 female healthy controls (100 from Yucatan and 100 from Central Mexico) were genotyped. Allelic and genotypic frequencies of variants were calculated and their association with lupus was analyzed. Results: Distribution of risk allele PTPN22 rs2488457G ranged 36% to 48%, while TRAF1-C5 rs10818488A and rs3761847G ranged from 34% to 40%. Heterozygous C/G was the most frequent for PTPN22 rs2488457 in all studied groups, while TRAF1-C5 heterozygous genotype was the most frequent in cases of Yucatan and controls from Central Mexico. However, we did not find significant differences in allelic and genotypic frequencies of PTPN22 and TRAF1-C5 variants, neither its haplotypes between cases and controls, suggesting a lack of association for lupus in the two Mexican populations. Conclusion: The PTPN22 rs2488457C˃G and TRAF1-C5 rs10818488A˃G and rs3761847G˃A variants do not confer susceptibility with the development of lupus in both studiedpopulations. However, the strong linkage disequilibrium observed in the TRAF1-C5 haplotypes suggests that they are co-inherited together and could be involved in the development of the disease in association with other genes or risk factors, as well as the Caucasian influence.