Abstract The rising attention globally on the use of oats and the beneficial effect of oat compounds in nutrition has also increased interest in oat production in Latvia. The aim of this study was to evaluate protein, amino acid and gluten content in husked and hulless oat grains grown in organic and conventional farming systems. Two hulless oat (Avena sativa L.) genotypes - the breeding line '33793' and the variety 'Stendes Emilija' and one husked oat variety 'Lizete' from the State Stende Cereal Breeding Institute - were cultivated in 2013 under conventional farming methods using three nitrogen (N) application rates (80, 120, and 160 kg·ha-1) and under organic farming. Protein content was determined by Kjeldahl method, amino acid composition by high-performance liquid chromatography method using Waters AccQ Tag, and gluten content by Sandwich R5 ELISA. The results showed that oat genotype had significant effect p < 0.001) on protein and gluten content, as well as on amino acid composition. The applied amount of fertiliser did not have significant effect on the studied quality parameters, but the growing system did (p < 0.001). Higher content of protein was observed in hulless oat samples, compared to that in husked oat samples. There was also a significant difference (p = 0.01) in the total amount of amino acids between husked and hulless oat samples. In hulless oat variety 'Stendes Emilija' and hulless breeding line '33793' the content of gluten was similar and two times higher than in the husked oat variety 'Lizete'. Further breeding work is necessary to obtain oats with a lower content of gluten-like proteins.