An integral part of a system that manages medical data is the persistent storage engine. For almost twenty five years Relational Database Management Systems(RDBMS) were considered the obvious decision, yet today new technologies have emerged that require our attention as possible alternatives. Triplestores store information in terms of RDF triples without necessarily binding to a specific predefined structural model. In this paper we present an attempt to compare the performance of Apache JENA-Fuseki and the Virtuoso Universal Server 6 triplestores with that of MySQL 5.6 RDBMS for storing and retrieving medical information that it is communicated as RDF/XML ontology instances over a RESTful web service. The results show that the performance, calculated as average time of storing and retrieving instances, is significantly better using Virtuoso Server while MySQL performed better than Fuseki.