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The purpose of this paper is to present a comparative study between a non-relational MongoDB database and a relational Microsoft SQL Server database in the case of an unstructured representation of data, in XML or JSON format. We mainly focus our presentation on exploring all the possibilities that each type of database offers us, in the case that the data, which has to be stored, cannot or is not wanted to be normalized. This is a scenario most often found in production when, for the application that is being developed we are extracting unstructured data from social networks or all kinds of different channels that the user might have. The comparative study is based on the creation of a benchmark application developed in C# using Visual Studio 2013, which accesses databases created beforehand with proper optimizations that will be described.