An integrated circuit with programmable transistors is programmed via a state machine on the integrated circuit. For example, the integrated circuit may be a programmable logic device, and the state machine may be a JTAG state machine. Each integrated circuit may have on it a register containing data indicating how long a particular programming operation should continue in order to be successful for that circuit. External programming control apparatus first reads that data and then at least partly bases the timing of programming instructions applied to the integrated circuit on that data. The integrated circuit may have an on-board programming voltage generating circuit which is turned on only by appropriate instructions from the external programming control apparatus. The external programming control apparatus controls the sequence and timing of all programming operations via the state machine port of the integrated circuit.