Samples from three different oat ( Avena sativa L.) cultivars, Vista, Gem and Dane were steeped and germinated in a pilot plant malting system. The content of avenanthramides, antioxidant compounds unique to oats, and some unknown compounds as well as the activities of the avenanthramide-synthesising enzyme hydroxycinnamoyl-CoA:hydroxyanthranilate N-hydroxycinnamoyl transferase (HHT) and the avenanthramide-oxidizing enzyme phenoloxidase (PO) were measured. An increase in avenanthramide content of germinated seeds, as compared to raw grains, was observed for Dane (125%, p < 0.001) and for Vista (29%, p = 0.007). The HHT activity increased 62% ( p = 0.014) in Dane, whereas no change was detected in Vista and Gem. The PO activity decreased slightly during the germination process for Gem ( p < 0.001) and Vista ( p = 0.005). Many of the unknown compounds increased significantly during germination in all three cultivars, and one of them was identified to be the avenanthramide N-(4′-hydroxy-3′-methoxy-( E)-cinnamoyl)-5-hydroxy-4-methoxyanthranilic acid. This study indicates that a highly controlled steeping and germination process can be a valuable method to increase the content of endogenous avenanthramides in oats.