Frankfurt segregates passengers a number of ways.

1. Departing passengers are segregated into Schengen and non-Schengen.

2. Arriving passengers from a Schengen flight are assumed to be 'secure' and are immediately mixed in with the departing Schengen passengers. So, if you are arriving from one Schengen destination and departing to another, you (normally) can walk to your gate without encountering any additional security.

3. Arriving non-Schengen passengers enter into a controlled area where they are screened before they are allowed into join the remainder of the international departures. If they are transferring to an international destination, they may do so without entering Germany. If they are transferring to a Schengen flight, or Frankfurt is their final destination, they exit the international departures area through immigration and customs for carry-on luggage, and then continue to either their Schengen gate, or to collect their luggage at arrivals.

4. They pass through customs again after collecting their checked luggage whether in Frankfurt, or in the case of transferring Schengen passengers, at their final destination.

5. While having to pass through customs twice sounds onerous, in fact, it is not, because the customs process is much simpler in Germany. There are no forms, and examinations are much rarer than in the United States.

Now, having explained the process logically, the question is how do they do it physically. Frankfurt tends to work mostly on a physical separation of the gates -- that is, one wing is reserved for Schengen, and one for non-Schengen. For countries which require special additional or special screening for departing passengers (Israel, Russia, and the United States at times) a separate wing is used to separate these passengers from others.

Munich uses a similar segregation approach but uses levels to separate domestic from international passengers.