The massive Pergamon Museum houses several departments, the most popular of which is probably the Department of Greek and Roman Antiquities, housed in the north and east wings of the museum.

Of special interest is the Pergamon Altar – an ancient Greek temple dating from 180-160BC – which is so huge that it has a room all to itself. The Near East Museum, in the south wing, contains one of the largest collections anywhere of antiquities from ancient Babylonia, Persia and Assyria.

The museum's upper level is devoted to the Museum of Islamic Art, containing many miniatures, carpets and woodcarvings.
Today, it accommodates three separate museums: the Antikensammlung (Collection of Classical Antiquities), occupying the architectural halls and the sculpture wing, the Vorderasiatisches Museum (Museum of the Ancient Near East) and the Museum für Islamische Kunst (Museum of Islamic Art). 

The Pergamon Museum houses some of the oldest reconstructed monumental buildings in the world. The highlight of the museum is the Pergamon Alta (built in second Century BC), which was transported and rebuilt from the original excavation site.

Staggered renovation work, begun in 2008, is currently under way as part of the Museum Island Master Plan, fulfilling plans devised by the architectural offices of Oswald Mathias Ungers. A total closure of the building will be avoided.