Mixing transactional and nontransactional statements within the same transaction.  In general, you should avoid transactions that update both transactional and nontransactional tables in a replication environment. You should also avoid using any statement that accesses both transactional (or temporary) and nontransactional tables and writes to any of them.

As of MySQL 5.1.44, the server uses these rules for binary logging:

Transactional, nontransactional, and mixed statements.  To apply those rules, the server considers a statement nontransactional if it changes only nontransactional tables, and transactional if it changes only transactional tables. A statement that changes both nontransactional and transactional tables is considered “mixed”. Mixed statements, like transactional statements, are cached and logged when the transaction commits.

Before MySQL 5.1.44, the rules for binary logging are similar to those just described, except that there is no binlog_direct_non_transactional_updates system variable to affect logging of transactional statements. Thus, the server immediately logs only the initial nontransactional statements in a transaction and caches the rest until commit time.

Before MySQL 5.1.31, the effect of the rules differs because the definition of transactional statement is different: In these earlier versions, a statement is nontransactional if the first changes it makes change nontransactional tables, transactional if the first changes it makes change transactional tables. “First” applies in the sense that a statement may have several effects if it involves such things as triggers, stored functions, or multiple-table updates. A mixed statement that changes both nontransactional and transactional tables is handled as nontransactional or transactional depending on the type of changes it makes first.

In situations where transactions mix updates to transactional and nontransactional tables, the order of statements in the binary log is correct, and all needed statements are written to the binary log even in case of a ROLLBACK. However, when a second connection updates the nontransactional table before the first connection transaction is complete, statements can be logged out of order because the second connection update is written immediately after it is performed, regardless of the state of the transaction being performed by the first connection.

Using different storage engines on master and slave.  It is possible to replicate transactional tables on the master using nontransactional tables on the slave. For example, you can replicate an InnoDB master table as a MyISAM slave table. However, if you do this, there are problems if the slave is stopped in the middle of a BEGIN ... COMMIT block because the slave restarts at the beginning of the BEGIN block.

Beginning with MySQL 5.1.48, it is also safe to replicate transactions from MyISAM tables on the master to transactional tables—such as tables that use the InnoDB storage engine—on the slave. In such cases (beginning with MySQL 5.1.48), an AUTOCOMMIT=1 statement issued on the master is replicated, thus enforcing AUTOCOMMIT mode on the slave.

When the storage engine type of the slave is nontransactional, transactions on the master that mix updates of transactional and nontransactional tables should be avoided because they can cause inconsistency of the data between the master transactional table and the slave nontransactional table. That is, such transactions can lead to master storage engine-specific behavior with the possible effect of replication going out of synchrony. MySQL does not issue a warning about this currently, so extra care should be taken when replicating transactional tables from the master to nontransactional tables on the slaves.

Beginning with MySQL Cluster NDB 6.2.14 and MySQL 5.1.24, every transaction (including autocommit transactions) is recorded in the binary log as though it starts with a BEGIN statement, and ends with either a COMMIT or a ROLLBACK statement. However, this does not apply to nontransactional changes; any statements affecting tables using a nontransactional storage engine such as MyISAM are regarded for this purpose as nontransactional, even when autocommit is enabled. (Bug #26395)