A stored procedure that uses LAST_INSERT_ID() does not replicate properly using statement-based binary logging. This limitation is lifted in MySQL 5.1.12.

Prior to MySQL 5.1.12, when a stored routine or trigger caused an INSERT into an AUTO_INCREMENT column, the generated AUTO_INCREMENT value was not written into the binary log, so a different value could in some cases be inserted on the slave.

An insert into an AUTO_INCREMENT column caused by a stored routine or trigger running on a master that uses MySQL 5.0.60 or earlier does not replicate correctly to a slave running MySQL 5.1.12 through 5.1.23 (inclusive). (Bug#33029)

Table-level AUTO_INCREMENT option values were not replicated correctly prior to MySQL 5.1.31. (Bug#41986)

Adding an AUTO_INCREMENT column to a table with ALTER TABLE might not produce the same ordering of the rows on the slave and the master. This occurs because the order in which the rows are numbered depends on the specific storage engine used for the table and the order in which the rows were inserted. If it is important to have the same order on the master and slave, the rows must be ordered before assigning an AUTO_INCREMENT number. Assuming that you want to add an AUTO_INCREMENT column to the table t1, the following statements produce a new table t2 identical to t1 but with an AUTO_INCREMENT column:

CREATE TABLE t2 LIKE t1;
ALTER TABLE t2 ADD id INT AUTO_INCREMENT PRIMARY KEY;
INSERT INTO t2 SELECT * FROM t1 ORDER BY col1, col2;

This assumes that the table t1 has columns col1 and col2.

The instructions just given are subject to the limitations of CREATE TABLE ... LIKE: Foreign key definitions are ignored, as are the DATA DIRECTORY and INDEX DIRECTORY table options. If a table definition includes any of those characteristics, create t2 using a CREATE TABLE statement that is identical to the one used to create t1, but with the addition of the AUTO_INCREMENT column.

Regardless of the method used to create and populate the copy having the AUTO_INCREMENT column, the final step is to drop the original table and then rename the copy:

DROP t1;
ALTER TABLE t2 RENAME t1;

See also Section B.1.7.1, “Problems with ALTER TABLE”.