Medical ontologies are valuable and effective methods of representing medical knowledge. In this direction, they are much stronger than biomedical vocabularies. In the process of medical diagnosis, each disease has several symptoms associated with it. There are currently no ontologies that relate diseases and symptoms and only attempts at their infancy along with some simple proposed models. However, well established ontologies for diseases and for symptoms were already developed in isolation. In this article, we are proposing an alignment algorithm to align the diseases ontology (DOID) with the symptoms ontology (SYMP) creating a core diseases symptoms ontology (DSO) that can scale to any number of diseases and symptoms The core DSO links a few diseases to their symptoms.