The brain development and performance of rats fed throughout two generations with an indigenous maize tortilla-based diet was studied. The experiment compared casein control with five different diets produced from: regular fresh masa; regular, enriched dry masa flour containing thiamin, riboflavin, niacin, folic acid, Fe and Zn (REDMF); dry masa flour fortified with 60 g/kg defatted soyabean meal and enriched (FEDMF); enriched quality protein maize (QPM) flour (EQPM); QPM flour fortified with 30 g/kg defatted soyabean meal and enriched (FEQPM). In both generations, brain and cerebellum weights and myelin concentration were significantly higher (P < 0.05) in rats fed the FEDMF and FEQPM diets. There was no significant difference (P > 0.05) in brain DNA in first-generation rats; however, second-generation rats fed FEDMF, EQPM and FEQPM tortillas had higher cerebral DNA, neuron size and brain activity as estimated by the RNA:DNA ratio. Short-term and long-term memory performance in the Morris maze improved (P < 0.05) among rats fed the FEDMF, FEQPM and EQPM diets. Second-generation rats fed the FEDMF and FEQPM diets had a superior (P < 0.05) working memory and learning performance. The utilisation of regular or QPM tortillas enriched with selected micronutrients and fortified with soyabean is highly recommended to assure adequate brain development. The high lysine-tryptophan QPM made it possible to save half of the soyabean flour without sacrificing the nutritional value of soyabean-fortified tortillas.