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This question already has an answer here:

I have a layover in Stockholm from the US on my way to the Czech Republic. I have both Czech and US passports. I need to pick up and recheck my bags. Will I need a transit visa?

marked as duplicate by JonathanReez Mar 21 '17 at 8:18

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Under the freedom of movement directive, Czech citizens have a near-absolute right to enter Sweden and stay indefinitely, and US citizens can enter visa-free for up to 90 days after a successful landing interview.

So simply present your Czech passport and the Swedish police practically cannot question you wanting to enter.

In fact, even if you didn't need to pick up baggage, the Schengen Area (of which Sweden and Czech form a part) is a single country for border purposes, so you'd clear immigration in Stockholm only regardless, and not in Prague - flights Stockholm-Prague are effectively domestic

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