MySQL replication works for InnoDB tables as it does for MyISAM tables. It is also possible to use replication in a way where the storage engine on the slave is not the same as the original storage engine on the master. For example, you can replicate modifications to an InnoDB table on the master to a MyISAM table on the slave.

To set up a new slave for a master, you have to make a copy of the InnoDB tablespace and the log files, as well as the .frm files of the InnoDB tables, and move the copies to the slave. If the innodb_file_per_table variable is enabled, you must also copy the .ibd files as well. For the proper procedure to do this, see Section 13.6.6, “Backing Up and Recovering an InnoDB Database”.

If you can shut down the master or an existing slave, you can take a cold backup of the InnoDB tablespace and log files and use that to set up a slave. To make a new slave without taking down any server you can also use the commercial InnoDB Hot Backup tool.

You cannot set up replication for InnoDB using the LOAD TABLE FROM MASTER statement, which works only for MyISAM tables. There are two possible workarounds:

Transactions that fail on the master do not affect replication at all. MySQL replication is based on the binary log where MySQL writes SQL statements that modify data. A transaction that fails (for example, because of a foreign key violation, or because it is rolled back) is not written to the binary log, so it is not sent to slaves. See Section 12.3.1, “START TRANSACTION, COMMIT, and ROLLBACK Syntax”.

Replication and CASCADE.  Cascading actions for InnoDB tables on the master are replicated on the slave only if the tables sharing the foreign key relation use InnoDB on both the master and slave. This is true whether you are using statement-based or row-based replication. Suppose that you have started replication, and then create two tables on the master using the following CREATE TABLE statements:

CREATE TABLE fc1 (
    i INT PRIMARY KEY,
    j INT
) ENGINE = InnoDB;

CREATE TABLE fc2 (
    m INT PRIMARY KEY,
    n INT,
    FOREIGN KEY ni (n) REFERENCES fc1 (i)
        ON DELETE CASCADE
) ENGINE = InnoDB;

Suppose that the slave does not have InnoDB support enabled. If this is the case, then the tables on the slave are created, but they use the MyISAM storage engine, and the FOREIGN KEY option is ignored. Now we insert some rows into the tables on the master:

master> INSERT INTO fc1 VALUES (1, 1), (2, 2);
Query OK, 2 rows affected (0.09 sec)
Records: 2  Duplicates: 0  Warnings: 0

master> INSERT INTO fc2 VALUES (1, 1), (2, 2), (3, 1);
Query OK, 3 rows affected (0.19 sec)
Records: 3  Duplicates: 0  Warnings: 0

At this point, on both the master and the slave, table fc1 contains 2 rows, and table fc2 contains 3 rows, as shown here:

master> SELECT * FROM fc1;
+---+------+
| i | j    |
+---+------+
| 1 |    1 |
| 2 |    2 |
+---+------+
2 rows in set (0.00 sec)

master> SELECT * FROM fc2;
+---+------+
| m | n    |
+---+------+
| 1 |    1 |
| 2 |    2 |
| 3 |    1 |
+---+------+
3 rows in set (0.00 sec)

slave> SELECT * FROM fc1;
+---+------+
| i | j    |
+---+------+
| 1 |    1 |
| 2 |    2 |
+---+------+
2 rows in set (0.00 sec)

slave> SELECT * FROM fc2;
+---+------+
| m | n    |
+---+------+
| 1 |    1 |
| 2 |    2 |
| 3 |    1 |
+---+------+
3 rows in set (0.00 sec)

Now suppose that you perform the following DELETE statement on the master:

master> DELETE FROM fc1 WHERE i=1;
Query OK, 1 row affected (0.09 sec)

Due to the cascade, table fc2 on the master now contains only 1 row:

master> SELECT * FROM fc2;
+---+---+
| m | n |
+---+---+
| 2 | 2 |
+---+---+
1 row in set (0.00 sec)

However, the cascade does not propagate on the slave because on the slave the DELETE for fc1 deletes no rows from fc2. The slave's copy of fc2 still contains all of the rows that were originally inserted:

slave> SELECT * FROM fc2;
+---+---+
| m | n |
+---+---+
| 1 | 1 |
| 3 | 1 |
| 2 | 2 |
+---+---+
3 rows in set (0.00 sec)

This difference is due to the fact that the cascading deletes are handled internally by the InnoDB storage engine, which means that none of the changes are logged.