Glover Garden (グラバー園, Glover-en) is an open air museum in Nagasaki that exhibits mansions of several of the city's former foreign residents and related buildings. It is located on the hill where Western merchants settled down after the end of Japan's era of seclusion in the second half of the 19th century. The main attraction of the garden is the Former Glover House, the oldest Western-style wooden building in Japan. Thomas Glover (1838-1911) was a Scottish merchant who moved to Nagasaki after the opening of its port to foreign trade in 1859. He later assisted some of the revolutionaries who would eventually overthrow the Tokugawa Shogunate in the Meiji Restoration. Active in various industries, including shipbuilding and mining, Glover features prominently in the early history of Japan's industrialisation.

Sofukuji Temple (崇福寺, Sōfukuji) is a temple in Nagasaki belonging to the Obaku school of Zen Buddhism. Originally built in 1629 for Nagasaki's Chinese residents, the temple is constructed in a Chinese architectural style and feels somewhat different to other temples in Japan. Sofukuji is built along the slope of a hill. At the bottom stands the temple's two-stories tall entrance gate, Ryugumon (lit. Gate of the Dragon Palace). Like the rest of the temple, it is painted bright red. The gate was originally built in 1673, but was destroyed several times by fire and storms before the most recent reconstruction was completed in 1849.

Dejima (出島) was a man-made island in the port of Nagasaki, constructed in 1636 to segregate Portuguese residents from the Japanese population and control their missionary activities. A few years later, the Portuguese were expelled from Japan, and the Dutch Trading Station, formerly located in Hirado, was moved to Dejima. The Dutch were restricted to Dejima during Japan's two centuries of isolation as the only remaining Westerners allowed in the country. Today, Dejima is not an island anymore, as the surrounding area has been reclaimed in the 20th century. However, a number of Dejima's historical structures remain or have been reconstructed in the area, including various residences, warehouses, walls and gates. The ultimate goal is to convert Dejima back into an island by digging canals around all its four sides.

Urakami Cathedral (浦上天主堂, Urakami Tenshudō) is a Catholic church in Nagasaki with a tragic yet interesting history. Today a working church housed in a large, European-style, red brick building, the cathedral is home to various relics that survived the atomic bombing. The atomic bomb was dropped on Nagasaki on August 9, 1945 and almost completely destroyed the church which stood only 500 metres from the hypocenter. A group of charred stone saints were left in place and still stand before a decimated wall in front of the cathedral. There are also other relics inside, including the surviving head of a Saint Mary statue recovered after the blast, and one of the church's original bells. The modern incarnation of the cathedral was completed in 1959.

Nagasaki Museum of History and Culture (長崎歴史文化博物館, Nagasaki Rekishi Bunka Hakubutsukan) is a well-executed, modern museum dedicated to Nagasaki's history as one of Japan's major international trading ports. The fairly large, permanent exhibition is spread over two floors and is comprised of various sections, each focusing on a different facet of Nagasaki's rich history. During the Edo Period the Japanese government adopted isolationism, effectively cutting the country off from the rest of the world. At this time, Nagasaki became one of the only ports where international trade was permitted, namely with the Chinese and Dutch. This temporarily made the city Japan's main window to the outside world and allowed a rich economy, culture and history to flourish.

Oura Church (大浦天主堂, Ōura Tenshudō) is a Catholic church in Nagasaki. Built towards the end of the Edo Period in 1864 by a French missionary for the growing community of foreign merchants in the city, it is considered the oldest standing Christian church in Japan. Oura Church is dedicated to the memory of the 26 Christians who were executed in the city in 1597. Today, the working church stands as an attractive example of contemporary European architecture, drawing many visitors. The church was the first Western-style building in Japan to be designated as a national treasure. The steep admission fee includes entrance to a museum about the history of Christianity in Japan.

Kofukuji Temple (興福寺, Kōfukuji) is the oldest and one of the most important Chinese-founded temples in Nagasaki. Located in the city's Teramachi ("Temple Town") district, it is the birthplace of the Obaku school of Zen Buddhism in Japan and has many interesting features. The temple was established around 1620 by a Chinese monk at a time when large numbers of Chinese merchants were coming to Nagasaki to trade. The complex was originally set up as a place to pray for safe sea travel for the merchants, and the construction is heavily influenced by Chinese architectural styles, making it feel different to other temples in Japan.

Nagasaki Confucius Shrine (孔子廟, Kōshi-byō) is one of only a handful of shrines dedicated to the revered Chinese philosopher Confucius in Japan. The shrine was built in 1893 by Nagasaki's Chinese community. The colourful, atmospheric shrine also contains a museum at the rear of the grounds. A small garden with a bridge and pond greets visitors at the entrance. The ornate Chinese-style buildings are adorned with yellow roofs. Flanking the shrine's courtyard stand the 72 sages, life-size stone statues that weigh around two tonnes each and depict Confucius' disciples. The shrine encourages visitors to find among the statues one that resembles a relative.

The Twenty Six Martyrs Monument and adjacent museum (二十六聖人記念館, Nijūroku Seijin Kinenkan) in Nagasaki are dedicated to the twenty six Christians who were executed here on February 5, 1597. They included both foreign missionaries and Japanese laymen. Missionary activities were prohibited at the time, and Japan's ruler Toyotomi Hideyoshi staged the execution as a warning. The monument is located in a small park on a hill not far from Nagasaki Station and offers nice views over the city. A straight red line runs from the monument across the park's plaza in the direction of the Oura Church on the opposite side of the city. Oura Church is also dedicated to the 26 martyrs.

The Dutch Slope (オランダ坂, Oranda-zaka) is a stone-paved street leading up a hillside in Nagasaki where many foreign traders resided after the opening of the city's port to foreign trade in 1859. Because the Dutch were the only Westerners allowed in the country for the preceding two centuries, "Dutch" referred to everything Western for a while. A few former residences remain in the area today. Among them, the Higashi Yamate 13 is open to the public. Once home to a well-to-do European family, this old Western-style house has been well preserved, with much of the old furniture and room layouts remaining. There is a balcony upstairs where nice views can be had of the surrounding area. A cafe is located on the ground floor.

Meganebashi (眼鏡橋, lit. Spectacles Bridge) is the most remarkable of several stone bridges that span the Nakashima River in city centre Nagasaki. The bridge, which gets its name from the resemblance it has to a pair of spectacles when reflected in the river water, is a popular tourist attraction and is designated as an important cultural property. The bridge was originally built in 1634, its construction overseen by the Chinese monk who would go on to become the resident priest of Kofukuji Temple, which is located a short walk away. The bridge, along with many of the others along the river, was badly damaged by floodwaters in 1982, but has since been repaired with recovered stones. There is a stone walkway along the river bank that makes for a pleasant stroll with nice views of the water and bridges. The walkway has a tranquil atmosphere and is accessed by steps from street level positioned at various points along the river.

The Nagasaki Prefectural Art Museum (長崎県美術館, Nagasaki-ken Bijutsukan) is a modern and spacious complex attractively located by the port of Nagasaki. The museum, which was designed by famous architect Kuma Kengo, opened in 2005 and contains permanent collections of art related to Nagasaki as well as a large collection of Spanish art. In addition, it also hosts temporary exhibitions.