Mandibular retrognathism may be the result of a developmental abnormality or the unfavorable positional relationship of developing jaws. Several lines of evidence suggest that muscles are known to have extensive mutual effects on bones. Studies with immunohistochemical staining and gene expression have shown unique combinations of myosin heavy chain isoforms in the masseter muscles. In this study, we aimed to evaluate MYO1H gene polymorphisms and haplotypes as risk factors for mandibular retrognathism.Twenty-five subjects with mandibular retrognathism and 25 control subjects of both sexes having an orthognathic maxilla (SNA, 82° ± 2°) between the ages of 12 and 30 years of age were selected for this study. Based on the cephalometric values, subjects with SNB angles smaller than 78° were considered to have mandibular retrognathism. Orthognathic subjects (SNB, 80°) without jaw deformations were used as the comparison group. Three polymorphisms of MYO1H gene (rs10850110, rs11611277, and rs3825393) were genotyped using polymerase chain reaction and restriction fragment length polymorphism. Associations were tested with the Pearson chi-square test and haplotype analyses.The single nucleotide polymorphism rs3825393 showed a statistically significant association with mandibular retrognathism. The cephalometric variables SNB and ANB angles showed significant differences among the various genotypes of rs3825393. Linkage disequilibrium was not strong and significant between the single nucleotide polymorphisms; hence, the haplotypes of the MYO1H gene are not associated with mandibular retrognathism.These results suggest that the rs3825393 polymorphism of the MYO1H gene is associated with an increased risk for mandibular retrognathism. The relatively small sample size used in the study resulted in modest statistical power. A parallel investigation on another population with larger samples to increase the power could further clarify the role of the MYO1H gene in causing mandibular retrognathism.