Can I program a 3.3v chip on a 5v board?
The clock speed selected will affect both delay*() and millis()/micros() as well as the functions in &lt;util/delay.h&gt;, therefore you must use the target system's correct clock speed if you are using any of these functions. This can be easily done by editing boards.txt and copying an existing entry for the Uno and changing the value of the f_cpu parameter to match the target system (in this case, 12000000).

The difference in voltage does not matter, since the chip can run at either voltage and no connection is being made between the 5V system and the 3.3V system.