Tokyo is the largest city on earth and packed with some of the world’s best shops, museums and restaurants, big and small. While the bright neon lights and the bustle of contemporary Tokyo may be what comes to mind when you think of the city, there is another side. Tokyo's historic gardens and neighborhoods of traditional homes on narrow lanes speak to a timeless Japan that has survived into the 21st century.

A thriving harbor town for centuries, Shimizu is best known for its incredible scenic beauty. Take an excursion to Miho no Matsubara and enjoy stunning views of Mount Fuji and expansive black sand beaches; stroll through the graceful gardens and unique art installations of Tokachi Millennium Forest; and visit Kongofukuji Temple, first built by Kobo-daishi in 822 and rebuilt from 1662.

Think of Osaka, Japan (accent on the O), as a combination of Los Angeles and Chicago. It very definitely has L.A.’s second-city complex, but its attitude is pure Chicago. The only business that matters is business, and so what if the Hanshin Tigers, the local baseball team, are frequently the worst professional athletes in the world? They’re the home team. People in Osaka laugh louder, play harder and drink more than Tokyo’s most decadent dreams. Osaka even has its own dialect, one the rest of the country calls “dirty Japanese,” one entirely different than even Kobe’s—and Kobe is an Osaka suburb. Nothing is old in Osaka. The place was flattened during the war (and then again in 1962 and 1989, by Godzilla). During the reconstruction, they forgot to include much in the way of parks or green space, and the sheer amount of concrete and steel sights can get overwhelming. But Osaka has its attractions and interesting things to do. Sumo wrestlers wait for trains, reeking of chanko-nabe (trad…

High atop a hill in Kochi sits 17th-century Kochi Castle, once the seat of the Yamauchi lords. Explore this historic site and enjoy panoramic views of the city, then dine on sushi at Hirome Market.

From the lively morning market of Asa-ichi, to the unparalleled views from Mount Hakodate, discover the history of the first Japanese port opened to international trade. Walk the ruins of the star-shaped Fort Goryokaku, the first of its kind in Japan, learn about local Ainu culture or simply feast on the abundance of fresh seafood this city is famous for.

Most Japanese used to think of Aomori merely as the place you caught the ferry to when you were going to Hokkaido. By the time you’d gotten here, they figured, you were pretty much at the edge of the civilized world. The small Tsugaru Strait that separates Honshu from Hokkaido isn’t big—only about 20 kilometers (12.5 miles) at its narrowest point—but it’s ecologically important: Hokkaido has animals related to northern Asia, whereas Honshu’s are more closely related to southern Asia’s. The strait is also famous for sudden, very rough weather and for no shortage of shipwrecks. The city was flattened in World War II, so there isn’t much history left to see. Still, it’s a lovely area, not much congestion or development, and because the town is still the major gateway to Hokkaido, the city has money to spend on architecture and parks. Its setting on the edge of Mutsu Bay means you will often be surprised by lovely water views through the buildings. The old way of thinking of Aomori is ove…

Set against a ruggedly beautiful coastline, Miyako is home to Jodogahama Beach, a picturesque pebble beach with rock outcroppings. Go for a swim then stop at Miyako Fish Market for a tasty lunch.

Tokyo is the largest city on earth and packed with some of the world’s best shops, museums and restaurants, big and small. While the bright neon lights and the bustle of contemporary Tokyo may be what comes to mind when you think of the city, there is another side. Tokyo's historic gardens and neighborhoods of traditional homes on narrow lanes speak to a timeless Japan that has survived into the 21st century.