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His explanation: The socket on which MySQL listens for new connections on a blocking socket most of the time but is set to non-blocking during the accept() of the new connection. Due to a bug in the kernel, the new socket returned by accept() is a blocking socket but returns the O_NONBLOCK flag when queried via fcntl(F_GETFL). That is, the file descriptor and the underlying socket don't agree on the blocking mode. Since MySQL determines via fcntl(F_GETFL) that the socket is non-blocking, it expects the first read() in my_real_read to not block, so it doesn't enable the timeout alarm. However, the read does block, and thus there's no timeout alarm. The thread kill (which relies on rescheduling the timeout alarm) also does not work as a consequence. The bug shows itself if you build MySQL with LinuxThreads support (needed for SMP on FreeBSD). Issuing a KILL command in MySQL won't be "noticed" by the "killed" thread until it runs another query--that makes KILL pretty useless. And the wait_timeout doesn't work either.