We present HyperGraphDB, a novel graph database based on generalized hypergraphs where hyperedges can contain other hyperedges. This generalization automatically reifies every entity expressed in the database thus removing many of the usual difficulties in dealing with higher-order relationships. An open two-layered architecture of the data organization yields a highly customizable system where specific domain representations can be optimized while remaining within a uniform conceptual framework. HyperGraphDB is an embedded, transactional database designed as a universal data model for highly complex, large scale knowledge representation applications such as found in artificial intelligence, bioinformatics and natural language processing. Key words: hypergraph, database, knowledge representation, semantic web, distributed