Model Driven Engineering (MDE) is a new approach that utilizes models as main artifacts for software development. Models facilitate the description of the problem in terms of its domain. However, since MDE is a new approach, it still has some drawbacks. One of them is model persistence. Commonly used tools can be inefficient to store and modify big models. Another problem is model representation. Models are usually represented in a graphical or textual notation and later they are stored in a completely different format . These formats may be inadequate to navigate and query the model. This paper addresses the above issues, utilizing graph-based databases to store and query models.