Physical abnormalities can be found in Down Syndrome patients. ALX3 gene mutations are result in frontonasal dysplasia. One of the peculiarities of facial anthropometry of Minangkabau women is the wide intercanthus distance when compared to Javanese and Batak women. A descriptive observational study was conducted on Down Syndrome patients and Minangkabau ethnicity aged 10-29 years who met the criteria as control. Data sampling of this study are taken by purposive sampling. Facial analysis using Rhinobase software. To examine the biomolecular analysis of ALX3 gene polymorphisms, sequencing was carried out using the Polymerase Chain Reaction (PCR) method. The average age of the sample was 17.7±4.8 years with 73% of the sample being male. There were significant differences in 14 of the 21 facial parameters. There was no significant difference in the En-En parameter with the mean intercanthus distance of the control group (39.25 mm) being greater than that of the SD group (38.07 mm). PCR examination results showed no polymorphisms were found in the ALX3 (rs121908169, rs121908168, rs387906319, rs121908170) and ALX3 (rs1570936479, rs121908166, rs34775503) genes in both groups. The largest distribution of samples based on gender was male. No significant difference found in the En-En parameter between the SD group and the control group. There were significant differences in 14 of the 21 facial parameters. There are no polymorphisms were found in the ALX3 in both groups.