If God created a perfect world, where do diseases come from?
In the beginning God made everything 'very good'. But since the Fall of man the entire universe has been degenerating. Many disease causing agents are the result of degeneration in organisms and mutations while others are the result of substances not doing what they would have in the world before sin.
Viruses, for instance, could have had a pre-Fall role in transferring genetic information to maintain genetic diversity.
For more information, there's a chapter in the Creation Answers Book that deals with this intriguing question.