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I'm considering of upgrading my current server to a new one and by default it comes with Mysql 5.x although have the option of continuing with old version as well. The question is can I just migrate without having to worry or will I need to make changes in my code/queries or table structures? There are a mix of table types, 48 MyISAM tables and 4 INNODB tables and DB's about 8 GB in size and I'm hoping that a change to Mysql 5.x will result in faster performance as well?

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While backward compatibility is a goal, there are always corner cases for which you need to research or test. Each version of the manual has a section on upgrading from the prior major release, so if you upgrade from 4.1 directly to 5.1 or 5.5, you should read the section for each major version upgrade. Each has general upgrade advice, and also a subsection on specific gotchas.

I would also recommend using a testing tool to check if the queries you use in your application have any regression failures or dramatic performance degradation between releases. A good free tool for this is pt-upgrade:

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