Genetic diversity and phenotypic knowledge of native maize (Zea mays L.) contribute to its use and conservation. Varieties of native maize (n=32), collected in the municipality of San Felipe del Progreso, Mexico State (Mexico), were studied in the current study. Maize grains of several different colours including white, yellow, white-yellowish, black and purple were analysed for grain structure, total content of phenols and anti-oxidant activity with the aim of assigning an added value to this native maize as well as considering the knowledge of its structure and anti-oxidant activity as a strategy for its conservation. Results showed that black coloured maize registered a fragile structure, the highest content of floury endosperm (80.34%), the lowest percentage of horny endosperm (4.8%), and were different to the rest of coloured varieties. The yellow maize varieties had the lowest anti-oxidant potential (32.3% of residual DPPH). No correlation between anti-oxidant potential and total content of phenols was found.