In many sequence learning tasks, such as program synthesis and document summarization, a key problem is searching over a large space of possible output sequences. We propose to learn representations of the outputs that is specifically meant for search: rich enough to specify the desired output but compact enough to make search more efficient. An appealing realization of such representation are discrete latent codes, as this naturally allows sophisticated combinatorial search strategies. The latent codes are learned using a self-supervised learning principle, in which first a discrete autoencoder is trained on the output sequences, and then the resulting latent codes are used as intermediate targets for the end-to-end sequence prediction task. Based on these insights, we introduce the Latent Programmer, a program synthesis method that first predicts a discrete latent codes from input/output examples, and then generates the program in the target language. We evaluate the Latent Programmer on two domains: synthesis of string transformation programs, and generation of programs from natural language descriptions. We demonstrate that the discrete latent representation significantly improves synthesis accuracy.