When you are developing website when it is needed to store and retrieve data from database whether it is small value in table or page content, you need to use server operation to retrieve, manage and perform any operation on database. Microsoft Sql server used in ASP.net and window based websites where MySql used in open source technology and development platforms. below are some points you should check while selecting.

The main difference in its usability My Sql is available free where You have to take license for Microsoft Sql. When it is low cost budget you don't have any option rather than choosing My Sql.

Microsoft Sql server supports windows XP and Window 2000 not the os lower than that and doesn't support Linux and oracle where MY Sql 2005 supports all version from 98 to XP and other OS like Linux, Unix and Mac.

My SQL is easier to maintain and install compare to MIctosoft SQL.

There are only few open source technology available which supports Microsoft SQL where there are good no. of platforms with My SQL.

InMicrosoft SQL , you can get design view from database in form of table and perform normal operation as you perform for table where it is not available in MYSQL.