Amaranth, quinoa and kañiwa are the most consumed Andean grains in Latin America, and possess high nutritional value as gluten-free substitutes for conventional cereals. The aim of this research was to examine the impact of these Andean grains on the sensory and physical properties of corn-based extruded snacks. Extrudates containing increasing contents of amaranth, quinoa or kañiwa (20, 35 and 50% of solids) were prepared under the same extrusion conditions. Extrudates with higher contents of amaranth, quinoa and kañiwa were rated less crispy, less crunchy and less adhesive with less hard particles. Temporal analysis showed that with increasing contents of amaranth, quinoa and kañiwa, crispiness and crunchiness were the most dominant attributes during mastication while the dominance of roughness reduced considerably. Porosity and wall thickness, measured by X-ray microtomography, were linked to the perception of crispiness and crunchiness, respectively. Despite the observable changes in the physical and sensory characteristics of extruded corn-based snacks, the incorporation of amaranth, quinoa and, particularly, kañiwa (the least studied Andean grain) showed promising results for the development of novel gluten-free products.