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I was exiting Schengen border on a member airport, and at passport control, the officer that was far from the computer just stamped my passport without registration of my exit on the system.

I asked and he said that system registration is only necessary on entrance and not on exit.

Is this right? Then, how do they assure that I have not overstayed?

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he said system registration is only necessary on entrance and not on Exit

If he actually said "system registration", he was wrong: there is no Schengen-wide "system registration" at all. When they scan your passport they just get a digital copy of your passport data along with possible alerts (such as arrest warrants) about the passenger, and they are supposed to do that on entry to the Schengen Area, and optionally on exit, though even on entry it's often not strictly followed, which really means nothing to you as a traveller.

Some countries have systems for their own use (which is not visible to the others), but it's still only the passport stamps that are the important thing. That's why you, as a non-EU/EFTA visitor, always have to make sure to get stamped when entering and exiting Schengen.

Sometimes, border agents (most commonly in France and Italy) will straight up lie and say it's "not needed" for "low-risk" passports (American, Australian etc.) because lifting their hand for a second seems to drain them of all life energy. They are breaking the law, however (specifically the Schengen Borders Code), by doing that, and you should never let them as you could get to pay for it.

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    There does appear to be newish (?) Schengen rules saying that passports have to be electronically scanned on entry to the area. At least Copenhagen Airport is plastered with posters in which the police apologize for longer waits at passport control, blaming such new rules. – Henning Makholm Feb 25 '18 at 12:23
  • @HenningMakholm Well yeah, but that doesn't mean the entries are recorded, just that the MRZ has to be systematically checked as a counter-fraud measure. And it's hardly taken seriously by all officers - since the rule was implemented I have, for example, entered Greece and Hungary by land, Germany, Italy and Sweden by air and the Euroairport (processed by a Swiss officer), and on many occasions they barely took my ID card in their hand. – Crazydre Feb 25 '18 at 12:46
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    x @Coke, the OP complained to the border guard that his passport was not scanned, and the border guard told him that passports are only scanned on entrance and not on exit. I see no reason to conclude from that, as you say that the border guard was wrong -- at most what is wrong is the OP's tacit assumption that the purpose of scanning the passport is to register it in an underlying system (and his therefore-inaccurate paraphrase of what the border guard actually said to him). – Henning Makholm Feb 25 '18 at 14:02
  • @HenningMakholm I get you, changed the wording. – Crazydre Feb 25 '18 at 14:30
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    @JanusBahsJacquet Also you cannot travel illegally as an EU/EFTA citizen, as you have an absolute right, by international law, to be in the EU and the Schengen Area. Hence no stamping. – Crazydre Feb 25 '18 at 21:53
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There's no Schengen-wide database of entries and exits. They ensure that you haven't overstayed by looking at the stamps in your passport. Yes, it's an imperfect system, but it is what it is.

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