If you don't want to change the port state or the loop of the program code (i.e. you want to react within 2 cycles from the signal arrival and can't afford any more instructions in the loop) you can always do this: Set up a timer interrupt, then perform this in the interrupt routine: Pop the return address (2 bytes), push address of the next instruction after the loop (or whatever routine you want to service the timeout instead) then RETI, the interrupt will cause the program flow to escape the loop as the return won't occur to where the interrupt happened, but wherever the last address on the stack points.