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I have searched the web a lot and could not find an answer that fits my situation. Here are two links that are quite contradictory:

My situation:
I visited Portugal in Dec 2012 for 29 days on a Schengen visa valid from Dec 1, 2012 to Feb 1, 2013 for research purposes (I am a Ph.D. student). I want to visit Sweden from Feb 10, 2013 to May 10, 2013 (89 days). I have applied for a Schengen visa again (for research). Will the 90/180 rule be applicable to me?

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What type of visa did you apply for for research? –  Karlson Jan 31 '13 at 14:55
    
Was it Schengen Type (C) visa? –  MeNoTalk Jan 31 '13 at 22:35
    
There are two websites which can help work out these kind of 90/180 visa rules in this older question: How to calculate stays against 90/180 visa rules? –  hippietrail Feb 1 '13 at 5:19
    
@Karlson I applied for a Schengen visa, but where it says "Purpose", i checked "Others" and mentioned "Research" in "Please specify". I always do that –  Prometheus Feb 1 '13 at 11:14
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As I understood it, the 90/180 rules is about when you're allowed to enter / when you must leave - it's not about whether you have one or several visas. –  hippietrail Feb 1 '13 at 11:27

4 Answers 4

up vote 14 down vote accepted

I got the visa today, so I am answering my own question for the benefit of others.
There indeed is a 90/180 day rule for Schengen visas. But the way the stay duration is calculated is a little different from what is seen in most forums on the web.

The 6 month (or 180 days to be precise) period starts on the day of the first entry into the Schengen zone (Note that the day of first entry means the day you physically arrive in the zone and not the day the validity of the visa starts). In that 6 month period, you can only stay in the Schengen zone for a maximum of 90 days, irrespective of whether you have a new Schengen visa issued by the same or a different Schengen country that is valid beyond this 6 month period. At the end of this 6 month period, a NEW 6 month period starts and you can again spend a maximum of 90 days in the Schengen zone, provided you have a valid visa. If your stay duration overlaps two 6 month periods, then you must individually satisfy the 90 day limit in BOTH periods. All following 6 months period will be calculated back to back from the date of the first entry, until you remain outside the Schengen zone for at least 6 months. When you stay outside for at least 6 months (continuously) and THEN enter the Schengen zone, the six month period again starts from the day of the entry. It would be as if you were entering the Schengen zone for the first time.

All this is based on page 63 of the Handbook for the processing of visa applications and the modification of issued visas, issued by the European Commission, and my experience with this visa.

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Wow this system of having "periods" with starting points is not at all how I thought the 60/180 rule worked! –  hippietrail Oct 16 '13 at 9:29
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+1 because it was originally correct (and very nice of you to follow-up on your earlier question) but this is not accurate anymore as of November 2013 (see the other answers). –  Relaxed Nov 11 '13 at 21:24

This may be a good question to visit a consulate of the destination country for.

Any information that I can find on the type C Schengen Visa is that it is 90 days in any rolling 180 day period.

There is only one site that has an indication that if you have entered EU for the purpose of business or conducting a research (see Annex 12) you may be exempt from the 90 days in 180 day requirement.

However in the border policies handbook nor in visa regulation documentation this particular exemption is explicitly stated.

So the more likely scenario in either the consulate or at the border is that the border control will err on the side of caution and indicate that you will violate your C visa by staying more then 90 days in 180 day period in the EU.

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Thanks for looking up all the rules! The links were helpful. I am still waiting for a decision from the embassy. I will update this post as soon as I get it. –  Prometheus Feb 4 '13 at 18:13
    
+1 as this now seems to be the interpretation used by at least some Schengen countries. –  Relaxed Oct 26 '13 at 13:17

The accepted answer was originally correct but the Schengen Borders Code has been amended by Regulation (EU) 610/2013 to counter the court's interpretation.

As of October 18, 2013 your stay should be “no more than 90 days in any 180-day period”. In particular, you should have been present less than 90 days during the past 180 days when leaving the Schengen area. Information about this is available on the website of the the EU commission along with a calculator

Also note that the new rules are in principle not applicable to citizens from the following countries: Antigua and Barbuda, The Bahamas, Barbados, Brazil, Saint Kitts and Nevis, Mauritius, and Seychelles. For these countries the old rules still apply because the visa waiver agreements still contain the older definition.

In any case, the rule always applies to a person. It does not matter if you have several passports, visas or nationalities.

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The official EU site now has a calculator to tell you how many days you can stay, after you input all your previous stays: http://ec.europa.eu/dgs/home-affairs/what-we-do/policies/borders-and-visas/border-crossing/schengen_calculator_en.html.

The UI is pretty weak, but it works.

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