Question: Are there disadvantages of using XML, instead of RDMS? The reason I ask this is because my data is more naturally represented by XML structure, rather than RDBMS. I initially thought of [storing the data in relational database](https://stackoverflow.com/questions/545145/map-xml-structure-to-database-schema), but the lack of flexibility of relational database to handle tree-like data structure was putting me of. So I am thinking about just storing the data in XML.

One thing I fear is performance penalty. While RDBMS can handle large datasets, I am not sure whether the same can be said about XML. Also, the database queries are pretty well-established and fairly easy to use and construct, what about XML queries? I don't know.

I am doing .Net application.

Answer: 
You should not compare XML with an RDBMS, since that are 2 complementary technologies; XML should not be considered, or regarded as a replacement for an RDMBS.

An RDMBS is for storing large amounts of data in a consistent way. The RDBMS should take care of the consistentcy of the data, etc ...

XML can be used for data-exchange between different computer systems for instance, but it should not be used to store large amounts of data over a long period of time.  

Xml doesn't allow you to take care of data-consistency like an RDMBS does; it doesn't take care of transactions, etc... Xml is actually nothing more then a text-file, that contains data in some kind of structured way.
Two big inherent advantages of RDBMS are:

1. Indexing. Greatly enhances performance.
2. Constraining. You can define relationships between elements which helps maintain the integrity of your data.

Keep in mind you can put xml in sql server and query it using xpath, so depending on the shape of your data, you may be able to get the best of both worlds.