Nowadays, automatic keyphrase extraction is considered to be an important task. Most of the previous studies focused only on selecting keyphrases within the body of input documents. These studies overlooked latent keyphrases that did not appear in documents. In addition, a small number of studies on latent keyphrase extraction methods had some structural limitations. Although latent keyphrases do not appear in documents, they can still undertake an important role in text mining because they link meaningful concepts or contents of documents and can be utilized in short articles such as social network service, which rarely have explicit keyphrases. In this paper, we propose a new approach that selects qualified latent keyphrases from input documents and overcomes some structural limitations by using deep belief networks in a supervised manner. The main idea of this approach is to capture the intrinsic representations of documents and extract eligible latent keyphrases by using them. Our experimental results showed that latent keyphrases were successfully extracted using our proposed method.