Methods, systems, and apparatus, including computer programs encoded on computer storage media, for neural translation systems with rare word processing. One of the methods is a method training a neural network translation system to track the source in source sentences of unknown words in target sentences, in a source language and a target language, respectively and includes deriving alignment data from a parallel corpus, the alignment data identifying, in each pair of source and target language sentences in the parallel corpus, aligned source and target words; annotating the sentences in the parallel corpus according to the alignment data and a rare word model to generate a training dataset of paired source and target language sentences; and training a neural network translation model on the training dataset.