Dark Ages: Holy Roman Empire has the same core mechanisms as Dark Ages: Heritage of Charlemagne, but it focuses on Central Europe. As a result, it has a different game board. In addition, the card mixes are different, with different unique Culture Cards for the rulers, technologies and units. Furthermore, Heritage of Charlemagne contains a set of Vassals, which are missing from Holy Roman Empire. Instead, this version has a set of Relics.
The two sets also differ in micro-expansions („modules“) that are included. Holy Roman Empire contains the Crusades and The Pope modules.