If choosing only one museum...

Hi Erika, I visited both sites you mentioned and didn't spend a lot of time at either one. The Unterlinden has the Isenheim Altarpiece and other religious works. Hotel Dieu is a medieval hospital. If I had to pick one, it would probably be the Hotel Dieu. Interesting history, beautiful architecture. Read up on both and see which one is most interesting to you.

I can't imagine going to Beaune and not visiting its most iconic site. It is an old hospital rather than a 'museum' in the traditional sense and you can visit it and see it in less than an hour.

Hotel Dieu.

The Unterlinden in Colmar is not like a Paris museum, no lines you just get a ticket and go in. Took me about an hour to see it and it was well worth it. The two museums are totally different and neither takes hours and hours to see so it would be very easy to see them both on your visits to those cities. I would do both.

Nancy has made an important point -- neither one require hours and hours of time -- and each is so emblematic and important in its respective city. If you're taking the trouble to go to each of these towns, you should go to both of those sites. Anyway, if you don't go to the Hotel Dieu in Beaune, you'll be disappointed because you'll be walking all around that gorgeous tiled roof and depriving yourself of going in!

I definitely agree that a visit to both museums is warranted. They are very different, easy to enter and navigate, are in the town centers and do not require an inordinate amount of time for a visit. If visiting the Orsay, I'd be there for 4-5 hours. Either of these museums should only require 1-1 1/2 hours for a visit.

I based in Avallon in Burgundy and in Eguisheim (just outside Colmar) in Alsace. I stopped in Beaune for 1/2 day on the way to Eguisheim. There's underground parking next to the TI - pick up a map, then a 10-minute walk through the center to the Hotel Dieu. I spent about 4-5 hours in Beaune and was satisfied with it. Loved the Hotel Dieu.

Thank you all - very good points that neither museum will take long. We will add both to our itinerary! Thanks again.
Erika

I've been to both and its a toss up. Unterlinden for art, but Colmar is so great to just walk around. Don't forget the Bartholdi museum is pretty neat too. Hotel Dieu is neat too for the buildings sake, and its story audio tour is a little wordy..

For what it's worth, RS has an episode where he visits the Hospice de Beaune and covers it pretty thoroughly. You could watch it and then decide if you want to see it in person. When we were there last year, we ended up skipping it in order to spend time in town wandering around.