All pins are 3.3V level, like an Arduino Due, whether they're being controlled from the SAM3X or i.MX6 CPU. They are *not* 5V tolerant, so you'll need a level-shifter circuit (e.g. 74LV245, FET-based equivalent, or simple resistor divider for input-only) to avoid the risk of damage when connecting 5V devices. Udoo Neo's are not out yet (still on track for September?), but I'm almost certain the situation will be the same on those as well.
