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If you love culture, archaeology, art, and history, Athens has some really exceptional museums! These are not listed in order of "best to worst" but rather in order that it makes sense to visit them if you're coming to Athens for a few days.
This museum, located in the fashionable district of Kolonaki and one of the "Kolonaki Museums" (see below), has a huge range of Greek art from the prehistoric period down to the modern period and everywhere in between. Come to get a good one-stop overview of the entirety of Greek art. This makes a very good "first stop" because once you leave here, you get more specialized. The Benaki has an excellent bookstore and often has interesting and off-beat temporary exhibitions.
Another of the Kolonaki Museums. Despite its name, this Museum, which has one of the largest collections of Cycladic art, has a lot besides, most notably the Cypriot art collection. There's a good general Ancient Greek art collection, and an exhibit on daily life in Ancient Greece. There are always temporary exhibits here, everything from showcasing modern Greek artists to the finds from a particular archaeological site to exploring a theme like Eros / Love in ancient Greece. The museum has a good bookshop and a very pleasant cafe.
If you've just come from the Benaki Museum and had your big overview, the very ancient collections in the Cypriot and Cycladic collections as well as the later Ancient Art and daily life in Ancient Greece collections will get you thinking about the early period of Greek history.
Another of the Kolonaki Museums, the Byznatine Museum has a large and beautifully curated collection of Byzantine architectural pieces, icons, ceramics, items from daily life, and items with religious function. The museum encourages you to see it slowly and thoughtfully, with widely spaced and uncluttered displays. You can relax in the shady garden courtyard before continuing on!
This surprisingly good museum, another of the Kolonaki Museums, is located next to the Byzantine Museum and deals with war history and equipment from antiquity to modern day.
Another of the Kolonaki Museums, although its location is technically not in Kolonaki but across the street from it, this is the best gallery of Greek paintings in the world. The collection begins with some El Greco works and then continues with early modern Greek painters whose focus was predominantly on nation-building / patriotic painting. The museum takes you through all phases of Greek painting up to the 80s. It's a very pleasant museum that is usually empty of visitors, and very much worth spending an afternoon! There's a cafe at the back and an excellent bookstore near the entrance. There is almost always an excellent temporary exhibition.
The last of the Kolonaki Museums, this is where you come to see Greece's largest collection of modern art. It exhibits both Greek (primarily) and also foreign artists' works in many media. After this museum, you've seen all the Kolonaki Museums and you've gone from prehistoric to modern!
The largest museum in the country and accepted as the most important, you need several visits or at least several hours to see this museum. I don't think you can see the whole thing at once, but you're welcome to try! Start in the central section with the Neolithic period, cross to the other side and see the Cycladic section, then go upstairs to the central area to see the Thira section; back downstairs to the center to see the Mycenaean section, and then follow the museum galleries around from Archaic to Classical; when you reach the beginning of the Hellenistic section, go to the Bronze collection, then upstairs, see the Ceramics Collection, finish that with a visit to the Jewelry and Cypriot sections, then back downstairs for the Hellenistic and Roman statuary! If you have time, check out the Egyptian gallery and whatever temporary exhibition is on.
There is a cafe with a nice leafy courtyard and a large bookstore. The museum is wheelchair accessible. Easiest way to get there is to take the trolley from Syntagma Square to the Polytechneio stop which is only a few meters away.
You're already at the National Archaeological Museum; just around the corner is the Epigraphical Museum. It's a museum mostly visited by scholars, but it's worth checking out if you're not completely museumed out by the National. Displaying only inscriptions (were you wondering why you didn't see any inscriptions at the National Museum? It's because they are all here), it gives you a great opportunity to see the evolution in Greek script as well as a quick ancient Greek civics lesson.
Jump on a trolley and head back to Syntagma area. Worth a visit is the beautiful Numismatic (Coin) Museum, which is in Heinrich Schliemann's house (he's the one who discovered Troy and Mycenae), and the house is worth a visit just to see the decoration. The coin exhibits are really interesting (I promise! They certainly have the potential to be boring, but they really aren't!) and cover all periods from very very ancient all the way down to the adoption of the Euro currency in 2002. There's a lovely cafe here, definitely worth a stop, and a very small bookshop.
Close to Syntagma Square, and another museum worth seeing just for the building alone, is the impressive National Historical, which is housed in the Old Parliament Building, and covers Greek history in the early modern and modern periods. Focussing primarily on the period just before, during, and after the War of Independence (1821-9) it is very undervisited and deserves to be on your list.
Heading down to Plaka via Kidathineon Street, you'll come to this unassuming yet enormous museum. It's full of folk art objects in silver, textiles, wood, and other materials from all of Greece. Their collection of costumes from around the country is excellent. There is a small shop at the entrance and periodic temporary exhibitions. The Theofilos (painter) exhibit is the highlight.
Taking the place of the original Acropolis Museum that was up on the Acropolis itself, this new museum (opened in 2009) is much larger and is able to display many more pieces that wouldn't fit into the old one. The museum covers not just the Parthenon, Propylaia, and Erechtheion, but also earlier buildings that were on the Acropolis before the Periclean building program, and also sanctuaries located all around the Acropolis slopes as well. It's one of the best museums for sculpture in the country.
On the other side of the Acropolis is the site of the Ancient Agora, which has its own small (but very good) museum. It's one of the best places to see some real objects of democratic Athens.
One of the most surprising and fascinating museums in the whole country is this little Plaka museum (free admission) which displays traditional musical instruments from the entire country broken down into categories based on how they produce sound. Listen to each instrument on headphones and visit the excellent store next door. It's opposite the Tower of the Winds.
Part of the Kerameikos site, this museum has lots of grave markers, including some of the most evocative and beautiful I've ever seen. It also has a great ceramics collection, since the Kerameikos, in addition to being the cemetery, was also the potters' quarter. This museum was recently reopened and is one of the most beautiful little museums in the city.