Title: Generative Discovery of Relational Medical Entity Pairs. Abstract: Online healthcare services can provide the general public with ubiquitous access to medical knowledge and reduce the information access cost for both individuals and societies. To promote these benefits, it is desired to effectively expand the scale of high-quality yet novel relational medical entity pairs that embody rich medical knowledge in a structured form. To fulfill this goal, we introduce a generative model called Conditional Relationship Variational Autoencoder (CRVAE), which can discover meaningful and novel relational medical entity pairs without the requirement of additional external knowledge. Rather than discriminatively identifying the relationship between two given medical entities in a free-text corpus, we directly model and understand medical relationships from diversely expressed medical entity pairs. The proposed model introduces the generative modeling capacity of variational autoencoder to entity pairs, and has the ability to discover new relational medical entity pairs solely based on the existing entity pairs. Beside entity pairs, relationship-enhanced entity representations are obtained as another appealing benefit of the proposed method. Both quantitative and qualitative evaluations on real-world medical datasets demonstrate the effectiveness of the proposed method in generating relational medical entity pairs that are meaningful and novel.