Introduction. The origin of the Jetyasar culture’s population remains a subject of debate. It was generally accepted that the Xiongnu penetrated into the Aral Sea region and participated in the formation of the local population. Previous studies have shown a complex and admixed origin of the Jetyasar people. But the spread of the head deformation tradition in this population imposes serious limitations on the application of craniometric methods for studying Jetyasar samples. Those limitations can be potentially mitigated with the use of geometric morphometrics (GM). The purpose of this work was to assess the degree of variation in the facial skeleton of the Jetyasar people in comparison with populations of the Early Iron Age and the Hunno-Sarmatian period. Material and methods. Digital, three-dimensional models of the skulls were created. Ten landmarks were placed on each of the models and subjected to general Procrustes analysis (GPA) and principal component analysis (PCA). Results. The first PC of the analysis of the total male sample reflects variation in the height of the face, nasal bridge protrusion, and the relative width of the infraorbital region. The second component describes the height of the lateral part of the zygomatic process of the maxilla and the adjacent part of the zygomatic bone. The Kosasar 2 male sample is the most diverse morphologically. This burial ground, according to archeological data, belonged to a migrant population related to the Xiongnu. In the female total sample, high values of the first PC are associated with a tall face, a weak nasal bridge protrusion, and a long zygomatic-maxillary suture. The second PC describes the morphology of the zygomatic process of the upper jaw. The Jetyasar samples are morphologically distinct from the skulls from China, Mongolia, Western Siberia, and Southern Siberia. An exception are the crania from the burial grounds of Kosasar 2, 3, and Altyn-Asar 4t which are similar to the early Iron Age samples from China (inner Mongolia, Warring States period, 5 th – 3rd centuries BC), Mongolia (Xiongnu period), and Tuva (Arzhan-2). Discussion. The Xiongnu migration could become a catalyst for the admixture and ethnogenetic processes in the region. Conclusion. Our study shows that the population of the Jetyasar culture was morphologically heterogeneous at all stages of the culture’s development. The hypothesis about the migrant roots of a part of the population is confirmed by our data.