A gluten-free diet is usually lacking in dietary fibre and minerals present in the bran and germ of grains. The aim of this work was to study the effects of different extrusion processes of whole grain maize flours (to avoid early rancidity development of the flours) in gluten-free cookies. Particle size and hydration capacity of the flours, rheology of the doughs, physicochemical characteristics, fibre content and sensorial analysis of the cookies were evaluated. The presence of whole-grain flours increased the particle size and the water absorption values. The elastic and viscoelastic modulus of the doughs decreased, allowing a greater expansion of the cookies in the oven, resulting in cookies with a higher spread ratio (reaching values of up to 12.2) and a lower hardness (decreasing in all cases more than 25% in relation to the Control). Cookies prepared with whole grain flours presented higher values of dietary fibre (< 8.4g/100g of lipid free cookie) and had a good acceptability. The extrusion of whole-grain maize flour has a positive impact on both in the shelf life of the flour (slower rancidity development) and in cookie quality.