Dentofacial deformities are characterized by abnormalities in craniofacial development that affects the individual's skeletal and occlusion, often causing functional and esthetic problems. In literature, there is an involvement of polymorphisms in estrogen receptor 1 (ESR1) and estrogen receptor 2 (ESR2) genes in craniofacial measurements. The aim of this study was to evaluate a possible association between polymorphisms in ESR1 (rs2234693 and rs9340799) and ESR2 (rs1256049 and rs4986938) genes with cephalometric measurements in individuals with dentofacial deformities. This cross-sectional study was performed with 158 individuals in the preoperative period of orthognathic surgery. The cephalometric measurements obtained through lateral cephalogram using Dolphin Imaging software. For genetic analysis, the DNA extracted from epithelial cells of the oral mucosa and were genotyped using the real-time polymerase chain reaction. The data found submitted to statistical analysis, through the Kolmogorov-Smirnov, Mann-Whitney, and Kruskal-Wallis tests, using the IBM SPSS software version 24.0. Considered a significance level of 0.05. We found association between polymorphisms and cephalometric measurements just in the female sex. The polymorphisms ESR1/ rs9340799 (P = 0.003), ESR1/rs2234693 (P = 0.026), and ESR2/rs1256049 (P = 0.046) were associated with the upper gonial angle (Ar-Go-N). The polymorphism ESR2/rs1256049 was also associated with the facial axis-rickets (NBa-PtGn) (P = 0.004), anterior cranial base (SN) (P = 0.036), and Y-axis (SGn-SN) (P = 0.031).