While an InnoDB secondary index is being created or dropped, the table is locked in shared mode. Any writes to the table are blocked, but the data in the table can be read. When you alter the clustered index of a table, the table is locked in exclusive mode, because the data must be copied. Thus, during the creation of a new clustered index, all operations on the table are blocked.

A CREATE INDEX or ALTER TABLE statement for an InnoDB table always waits for currently executing transactions that are accessing the table to commit or roll back. ALTER TABLE statements that redefine an InnoDB primary key wait for all SELECT statements that access the table to complete, or their containing transactions to commit. No transactions whose execution spans the creation of the index can be accessing the table, because the original table is dropped when the clustered index is restructured.

Once a CREATE INDEX or ALTER TABLE statement that creates an InnoDB secondary index begins executing, queries can access the table for read access, but cannot update the table. If an ALTER TABLE statement is changing the clustered index for an InnoDB table, all queries wait until the operation completes.

A newly-created InnoDB secondary index contains only the committed data in the table at the time the CREATE INDEX or ALTER TABLE statement begins to execute. It does not contain any uncommitted values, old versions of values, or values marked for deletion but not yet removed from the old index.

Because a newly-created index contains only information about data current at the time the index was created, queries that need to see data that was deleted or changed before the index was created cannot use the index. The only queries that could be affected by this limitation are those executing in transactions that began before the creation of the index was begun. For such queries, unpredictable results could occur. Newer queries can use the index.