Objective: To determine the correlation between polymorphisms of ACTN3 R557X and Q523R genes on skeletal patterns in Indonesian Subpopulations. Material and Method: The subjects were 171 patients with class I, II, and III skeletal malocclusions at the Faculty of Dentistry, Universitas Indonesia. Research samples consisted of 10 hair follicles and lateral cephalometric photographs of the patients. DNA sequence amplification was carried out using the Polymerase Chain Reaction (PCR) and followed by Restriction Fragment Length Polymorphism (RFLP) analysis. Skeletal patterns were determined based on a radiographic analysis of the initial cephalometry using the ANB, Facial axis, and Gonion angle. Results: The distribution of genotypes and alleles showed that the highest frequency was found in the heterozygous genotype group compared to the other homozygous genotypes in all groups. In general, the genotype difference between R557X and Q523R only occurred in 5 samples, or 3% of the total number of research subjects. Conclusion: There is no correlation between the ACTN3 R557X and Q523R gene polymorphisms with skeletal malocclusion class I, II, and III, vertical facial growth, and growth direction of the lower third of the face. However, it is found that ACTN3 R557X and Q523R in the Indonesian subpopulation experienced linkage disequilibrium. © 2025 JDMFS. Published by Faculty of Dentistry, Hasanuddin University. All rights reserved.