Ever since the 16th century christian traders visited the harbours of Sumatra, and franciscan munks served the foreign community in Aceh. The only populations which were allowed to convert during the colonial period were those who showed fierce resistance against the islam, especially in the Batak highlands and the Niha (from the island Nias).
In the 19th century, several missionaries made the dangerous trip to the Batak area. Some were not lucky. In 1824, two members of the English Baptist Mission Society, Burton and Wars, translated pieces of the bible in Batak, and spend a week in the Silindungvalley, but they were prohibited to go ahead, because England gave away Sumatra to the Dutch. The French catholic mission in Penang tried to spread their area over Nias in 1832, but the first two priests, Vallon and Berard, died shortly after they had arrived at Gunungsitoli.
Two Americans, Lyman and Munsin, travelled to the Silindung valley, where they were killed in 1834. A number of Dutch missionaries worked in the southern part of the Batak area round 1850, at that time under Dutch rule, but they were not very successfull, because the area already was mostly islamic.
The big Dutch linguist van der Tuuk (he himself was partially mixed origine) was the first European to actually see Danau Toba. However he was appointed as biblic translator, the excentric scientist didn't have much interest in spreading christianity, but instead of that he spend his time making a dictionary and grammar for the Toba Batak linguage.
After the decision of the german 'Rheinische Missions Gesellschaft' (RMG) in 1861 to start working in the Batak highlands, and with the arrival of Ludwig Nommensen, the first christianization really started. He helped the Toba Batak as a doctor, negotiator and teacher. From the Silindung valley he spread his work towards the north. His efforts were rewarded, entire communities converted in the years after 1880. Towards 1900 the Toba Batak mainly were protestant, and christianity seemed to be a part of the Batak identity.
As a reaction on this, several movements which tried to combine christianity, islam and traditional religions, with Sisingamangaraja as liberator.The Parmalim movement florished at the end of the 19th century south and east of Danau Toba, while the militant Parhudamdam movement threathened the plantations in the First World War.
Growing resistance against the, as some say, paternalistic rule of the European missionasies lead to an independent church in 1927, the Huria Kristen Indonesia (HKI), was formed. As a reaction the Rheinische Mission was reformed into an autonomous Batak church in 1930.
In contrary to the somekind small position of christians in many parts of Asia, the three milion Toba Batak are sure of their status as Indonesian nationalists which have played their role in the revolution and now have an important place in the Indonesian military and politics.
Among the Karo and Simalungun, christianity spread much slower, partially because it was first associated with Dutch colonial rule and later with that of the Toba Batak. In 1940 only 5000 Karo were converted. The forced departure of the Dutch missionaries during the Japanese occupation seemed to be a stimulating factor for the Karo church, and after the suppression of the communism in 1965 the Karo converted en masse to christianity, started by the distress by the Indonesian government on everyone which 'does not have a religion with only one God and one holy book'.
On Nias the mission started with the systematical Dutch rule over the island since 1890. Towards 1915 there were almost 20,000 Miha christians, against 1940 the bigger part, about 135,000 people, were converted to christianity. Catholics were abolished from missions in the Batak highlands until the 1930's, but after that they became famous very fast. Nowadays more than ten per cent of the population is catholic.