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The problem with slow queries on PHP when dealing with large amounts of data in MySQL tables is that PHP has to wait for the MySQL server to process the query before it can proceed with the next step in the PHP script. If the query is slow, this can cause the PHP script to appear unresponsive to the user, and lead to longer load times and decreased performance. Additionally, slow queries can cause database locks, which can prevent other queries from being executed, leading to further delays and performance issues.