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Kutna Hora
Things to Do  

Kutna Hora is nice. It's touristed but not overrun. I thought the cathedral was gorgeous, and that's saying something because I got pretty sick of looking at cathedrals during 6 months of travel. The Italian Court, where Bohemian coins were minted in the middle ages, was very interesting. The famous bone church of Sedlec is a quick bus ride away. I wouldn't put Kutna Hora at the top of your must-see list, but it did play an important role in Czech history. It's probably worth a day or two.

The old mine freaked me out, but I'm scared pretty easily.

I didn't make it to Jihlava, but it was highly recommended by my professors.