The FOREIGN_KEY_CHECKS, SQL_MODE, UNIQUE_CHECKS, and SQL_AUTO_IS_NULL variables are all replicated (this has been true since MySQL 5.0). The storage_engine system variable (also known as table_type) is not yet replicated in MySQL 5.1, which is a good thing for replication between different storage engines.

Session variables are not replicated properly when used in statements that update tables. For example, SET MAX_JOIN_SIZE=1000 followed by INSERT INTO mytable VALUES(@@MAX_JOIN_SIZE) will not insert the same data on the master and the slave. This does not apply to the common sequence of SET TIME_ZONE=... followed by INSERT INTO mytable VALUES(CONVERT_TZ(...,...,@@time_zone)).

Replication of session variables is not a problem when row-based replication is being used. See Section 6.1.2, “Replication Formats”.