Upstairs is a permanent exhibit that takes you through the history of Honduras beginning basically from the prehistoric period, as well as a couple of smaller rooms for seasonal art exhibits. The information is only in Spanish but there is at least one English-speaking tour guide who is very knowledgable and friendly.
Downstairs there is a small theater showing an excellent 3D animated video of the Mayan ruins at Copan. It is of course in Spanish but interesting to watch as it shows you how the ruins are thought to have looked originally compared to what they look like today. They have two or three showings at set times each day.
They also have a pretty decent gift shop, and the relatively clean bathrooms (most of the time with toilet paper!) are definitely worth a mention.
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