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I want to use a ATmega (168 or 328) with a 3V button cell. Which isn't the problem but at the moment I think about how to make it pogrammable in the target board. The board will have some peripheral devices like leds which can't operatet at a higher voltage.

So can a normal ISP programmer or even a USB to TTL adapter be used to programm this 3V system?

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You can find USB to TTL adaptors that are 3.3v compliant (Use your power source not the one provided by the adaptor)

and some ISP programmers will have a jumper to choose the voltage

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