If you are visiting Prague before September 2013, you really should visit the Veletrzni Palace to see the exhibition of Mucha's 'Slav Epic'. Words can't really do it justice, but opportunities to view the complete collection are rare (it still doesn't have a proper home, a century after some of the paintings were completed).
The permanent collection in the museum is also worth visiting. In addition to some high-profile non-Czech pieces, there are some wonderful paintings and sculptures by Czech artists that perhaps you haven't heard of.
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