Abstract The attentional mechanism has proven to be effective in improving end-to-end neural machine translation. However, due to the intricate structural divergence between natural languages, unidirectional attention-based models might only capture partial aspects of attentional regularities. We propose agreement-based joint training for bidirectional attention-based end-to-end neural machine translation. Instead of training source-to-target and target-to-source translation models independently, our approach encourages the two complementary models to agree on word alignment matrices on the same training data. Experiments on ChineseEnglish and English-French translation tasks show that agreement-based joint training significantly improves both alignment and translation quality over independent training.