Originally Posted by corporate-wage-slave

If you are arriving from outside Schegen (e.g. USA - LIS) and are transferring to PRG then you clear Schengen immigration in LIS. They can be lines during the morning peak. If you are doing a transit to PRG from inside Schengen, e.g. MAD-LIS-PRG then there are no passport controls, you walk to the departing gate with no checkpoints.