Takayama: Located in the Japan Alps and surrounded by mountain peaks, this former castle town has a delightful historic quarter with 18th-century merchant homes, sake breweries, special-interest museums, craft shops, restaurants, and Japanese inns, all easy to explore on foot. Another highlight is the Hida Minzoku Mura Folk Village, an open-air museum illustrating how local farmers once lived.

Ogimachi (Shirakawago): With its thatch-roofed farmhouses, paddies trimmed with flower beds, roaring river, and pine-covered mountains rising on all sides, Ogimachi is one of the most picturesque rural villages in Japan. Many of the large, thatched farmhouses are now inexpensive minshuku (family-run inns), where you can stay and sample the local mountain cuisine.

Tsumago: Nestled in the Japan Alps, Tsumago served as an old post town for daimyo (feudal lords) and their samurai traveling between Kyoto and Edo (now Tokyo). Virtually untouched by the 20th century, it has many authentic feudal-age wooden buildings, some of which are open to the public.

Nara: This ancient capital boasts a large park with temples, shrines, museums, and the country's largest bronze Buddha, plus friendly free-ranging deer.

Mount Koya: This mountaintop enclave of 120 Shingon Buddhist temples is one of Japan's most sacred places. It contains the mausoleum of Kobo Daishi, one of the most revered figures in Japanese Buddhist history, as well as an extensive burial ground of daimyo, samurai, and others who wished to be close to their leader for eternity. Following in the footsteps of emperors, nobles, and commoners who've made pilgrimages here over the last thousand years, you can even spend the night in one of the temples.

Uchiko (Shikoku): This well-preserved village boasts a number of buildings dating from the Edo Period and the turn of the 20th century, including several homes now open to the public and a 1916 Kabuki theater.