Buddhism is the second oldest religion in Indonesia , arriving around the sixth century. The history of
Buddhism in Indonesia is closely related to the history of Hinduism, as a number of empires based on Buddhist culture were established around the same period. Indonesian archipelago has witnessed the rise and fall of powerful Buddhist empires such as Sailendra dynasty, Sriwijaya and Mataram Empires.
The arrival of Buddhism was started with the trading activity that began in the early of first century on the Silk Road between Indonesia and India . According to some Chinese source, a Chinese traveler monk on his journey to India , has witnessed the powerful maritime empire of Sriwijaya based on Sumatra .
The empire also served as a Buddhist learning center in the region. A number of historical heritages can be found in Indonesia , including the Borobudur Temple in Yogyakarta and statues or prasasti (inscriptions) from the earlier history of Buddhist empires.
According to the 1990 national census, slightly more than 1% of the total citizens of Indonesia are Buddhists, which takes up about 1.8 million people. Most Buddhists are concentrated in Jakarta , although other provinces such as Riau, North Sumatra and West Kalimantan also have a significant number of practitioners. However, these totals are likely high, due to the fact that practitioners of Confucianism and Taoism, which are not considered official religions of Indonesia , referred to themselves as Buddhists on the census.
Hindu culture and religion arrived in the Indonesian archipelago in the first century, later coinciding with the arrival of Buddhism, resulting in a number of Hinduism-Buddhism empires such as Kutai, Mataram and Majapahit. The Prambanan Temple complex was built during the era of Hindu Mataram, during the Sanjaya dynasty. The greatest Hindu empire ever flourished in Indonesian archipelago was Majapahit empire. The age of Hindu-Buddhist empires lasted until the sixteenth century, when the archipelago's Islamic empires began to expand. This period, known as the Hindu-Indonesia period, lasted for sixteen full centuries. The influence of Hinduism and classical India remain defining traits of Indonesian culture; the Indian concept of the god-king still shapes Indonesian concepts of leadership and the use of Sanskrit in courtly literature and adaptations of Indian mythology such as the Ramayana and Mahabharata.
Hinduism in Indonesia takes on a tone distinct from other parts of the world. For instance, Hinduism in Indonesia , formally referred as Agama Hindu Dharma, never applied the caste system. Another example is that the Hindu religious epics, the Mahabharata (Great Battle of the Descendants of Bharata) and the Ramayana (The Travels of Rama), became enduring traditions among Indonesian believers, expressed in shadow puppet (wayang) and dance performances. Hinduism has also formed differently in Java regions, which were more heavily influenced by their own version of Islam, known as Islam Abangan or Islam Kejawen.
All practitioners of Agama Hindu Dharma share many common beliefs, mostly the Five Points of Philosophy: the Panca Srada. These include the belief in one Almighty God, belief in the souls and spirits and karma or the belief in the law of reciprocal actions. Rather than belief on cycles of rebirth and reincarnation, Hinduism in Indonesia is concerned more with a myriad of local and ancestral spirits. In addition, the religion focuses more on art and ritual rather than scriptures, laws and beliefs.
The official number of Hindu practitioners is 6.5 million (2006),  making up about 1.8% of all Indonesians, and currently giving Indonesia the fourth largest number of Hindus in the world. This number is disputed by the representative of Hinduism in Indonesia , the Parisada Hindu Dharma. The PHDI gives an estimate of 18 million.  Of this number, 93% of the practitioners are located in Bali , the majority of the population of which is Hindu. Besides Bali, Sumatra, Java, Lombok and Kalimantan island also have significant Hindu populations. Central Kalimantan is 15.8% Hindu.
Indonesia is the world's most populous Muslim-majority country, with 88 percent of its citizens identifying as Muslim. Traditionally, Muslims have been concentrated in the more populous western islands of Indonesia such as Java and Sumatra. In less populous eastern islands, the Muslim population is proportionally lower.
The history of Islam in Indonesia is complex and reflects the richness and diversity of Indonesian cultures. In the 12th century many predominantly Muslim traders from India arrived on the island of Sumatra, Java and Kalimantan where the religion flourished between the twelfth and fifteenth centuries. The dominant Hindu and Buddhist kingdoms of the time, such as Majapahit and Sriwijaya, were in decline and the numerous Hindus and Buddhists mostly converted to Islam, although a smaller number, as in the notable case of Hindus immigrating to Bali, moved off Java and Sumatra. Islam in Indonesia is in many cases less meticulously practiced in comparison to Islam in, for example, in the Middle East region
Confucianism originated from China mainland and brought by Chinese merchants and immigrants. It is estimated as late as the 3rd century AD that the Chinese arrived in Nusantara archipelago. Unlike other religions, Confucianism evolved more into loose individual practices and belief in the code of conduct, rather than a well-organized community religion, or way of life or social movement. It was not until the early of 1900s that Confucianists formed an organization, called Tiong Hoa Hwee Koan (THHK) in Batavia (now Jakarta ).
After the independence of Indonesia in 1945, Confucianism in Indonesia was affected by several political turmoil's and has been used for some political interests. In 1965, Sukarno issued Presidential Decree No. 1/Pn.Ps/1965, in which there be six religions embraced by the Indonesian people, including Confucianism. Earlier in 1961, the Association of Khung Chiao Hui Indonesia (PKCHI), a Confucianist organization, declared that Confucianism is a religion and Confucius is their prophet.
Hence the status of Confucianism in Indonesia in the New Order era was never clear. De jure, there were conflicting laws, as the higher law permitted Confucianism, but the lower law did not recognize it. De facto, Confucianists were not recognized by the government and they were forced to become Christians or Buddhists to maintain their citizenship. This practice was applied in many places, including in the national registration card, marriage registration, and even civics education in Indonesia taught school children that there are only 5 official religions.
With the fall of Suharto in 1998, Abdurrahman Wahid was elected as the fourth president. Wahid lifted the Presidential Instruction No. 14/1967 and the 1978 Minister of Home Affairs directive. Confucianism is now officially recognized as religion in Indonesia . Chinese culture and all related Chinese-affiliated activities are now allowed to be practiced. Chinese and non-Chinese Confucianists have since then expressed their belief in freedom.
The Government of Indonesia officially recognizes the two main Christian divisions in Indonesia , Protestantism and Roman Catholicism , as two separate religions.
Protestantism arrived in Indonesia during the Dutch East Indies (VOC) colonization, around the sixteenth century. VOC policy to ban Catholicism significantly increased the percentage of Protestant believers in Indonesia . Missionary efforts for the most part did not extend to Java or other already predominantly Muslim areas. The religion has expanded considerably in the 20th century, marked by the arrival of European missionaries in some parts of the country, such as Western New Guinea and Lesser Sunda Islands . Following the 1965 coup, all non-religious people were recognized as Atheist, and hence did not receive a balanced treatment compared to the rest of the citizens. As a result, Protestant churches experienced a significant growth of members, partly due to the uncomfortable feeling towards the political aspirations of Islamic parties.
Protestants form a significant minority in some parts of the country. For example, on the island of Sulawesi , 17% of the citizens are Protestants, particularly in Tana Toraja and Central Sulawesi . Furthermore, up to 65% of the Torajan population is Protestant. In some parts of the country, entire villages belong to a distinct denomination, such as Adventist, Lutheran, Presbyterian or Salvation Army (Bala Keselamatan) depending on the success of missionary activity. Indonesia has two Protestant-majority provinces, which are Papua and North Sulawesi , with 60% and 64% of the total population consecutively. In Papua, the faith is most widely practiced among the native Papuan population. In North Sulawesi, the Minahasan population centered around Manado converted to Christianity in the nineteenth century. Today most of the population native to North Sulawesi practice some form of Protestantism, while transmigrants from Java and Madura practice Islam. As of 2006, 6% of the total citizens of Indonesia are Protestants.
Catholicism arrived in Indonesia during the Portuguese arrival with spice trading. Many Portuguese had the goal of spreading Roman Catholicism in Indonesia , starting with Maluku islands in 1534. Between 1546 and 1547, the pioneer Christian missionary, Francis Xavier, visited the islands and baptized several thousand locals.
During the Dutch East Indies (VOC) era, the number of Roman Catholicism practitioners fell significantly, due to VOC policy to ban the religion. The most significant result was on the island of Flores and East Timor , where VOC concentrated. Moreover, Roman Catholic priests were sent to prisons or punished and replaced by Protestant priests from the Netherland. One Roman Catholic priest was executed for celebrating Mass in a prison during Jan Pieterszoon Coen's tenure as Governor-General of the Dutch East Indies .
As of 2006, 3% of all Indonesians are Catholics, slightly lower than the total number of Protestants. The practitioners mostly live in Papua and Flores.
On September 22, 2006, there was a massive strike by Catholics, concentrated mainly on Flores Island following the execution of three Roman Catholic men. Fabianus Tibo, Marinus Riwu, and Dominggus da Silva were convicted in 2001 of leading a Christian militia which killed at least 70 Muslims in 2000. However, human rights groups had questioned the fairness of the trial: claiming that although the three participated in the militia, they were not the leaders.