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I have started a project that size matters so i got Arduino mini and all i need to do it have it communicating with another Aurduino mini via xbees. Now i also need to be able to know how long it takes for signal to be sent and back and considering they are max 50 ft apart, that will bring the time down to ns, which internal timer on Arduino wont be able to do it.

I've never used an Xbee, or done anything that time-critical with the Arduino, so this just my intiuition... I don't think the distance has anything to do with it, and I suspect it's going to be a LOT slower than you think... You are not just bouncing a signal off the wall...

For example, let's say we are 50ft apart and I ask you, "Can you hear me?" It takes about 50mS for my question to reach you, and about 50mS for the answer to return. But that doesn't matter, because it takes much longer to ask the question, for you to process/understand the question and respond, and for me to process/understand the answer.