The rice flour and corn starch mixture used in the gluten-free cake formulation was replaced with chia flour (CF) and quinoa flour (QF) up to 25% CF and 25% QF level. The effects of CF and QF on the physical, chemical and sensory properties of gluten-free cakes were investigated. CF and QF replacement increased the ash, protein, fat, total phenolic content and antioxidant capacity of gluten-free cakes by 1.5, 1.8, 1.3, 3.5 and 2.9 times, respectively, when compared to the control samples. Statistically significant increases were found in Ca, P, K, Mg, Fe and Zn contents of cake samples (P <0.05). The cakes containing CF and QF, received higher texture and taste-odour scores than control. According to the sensory analyses results it can be concluded that QF and CF can be used in gluten-free cakes up to 20% and 20% levels, respectively.