The aim of this work was to test the association between estrogen receptor α gene (ERα) polymorphism and primary osteoarthritis (OA) of the knee in Mexican mestizo patients. A case-control study was conducted. Cases were patients >40 years of age, with a body mass index (BMI) ≤ 27 and radiologic score for OA of the knee of ≥2 according to Kellgren-Lawrence scale, and controls were subjects >40 years age with a radiologic score <2. Two restriction fragment length polymorphisms, PvuII (T/C; rs2234693), and XbaI (A/G; rs9340799), of the ERα were analyzed. Allelic haplotypes were constructed and non-conditional logistic regression was developed to evaluate risk magnitude through odds ratios (ORs) and 95% Confidence intervals (95% CI). Three different allelic haplotypes were identified: TA; CG, and CA. Unadjusted analysis of the haplotypes did not show significant associations; nonetheless, when data were adjusted for gender, age, and BMI, a significant decrease risk was observed for CG haplotype (OR [95% CI]) = 0.5 (0.3-0.9)] (P = 0.04). These results suggest that ERα gene CG haplotype could be associated with a reduced risk of primary knee OA in Mexican mestizo population.