After having been dependent upon the Sultan of Banten for more than a decade, the Dutch East India Company (VOC), or rather its governor general Jan Pieterszoon Coen, decided in 1617 to build their own premises at the place where present-day North Jakarta is located. A map of 1627 shows that Batavia, as the new town was called, was basically a fortress and a walled area with warehouses and residences. It had no more than five to six thousands inhabitants, including some 700 Dutchmen, a multi-ethnic garrison, many Chinese and slaves from all over Asia. They lived in a town that was built in Dutch fashion. That meant canals for the transportation of merchandise, compact buildings for offices and living quarters, and inevitably, windmills and draw bridges. As the settlers were soon to find out, under tropical conditions the houses proved to be suffocating and the canals pestilentious as well as an agreeable home to local crocodiles.

The new town faced a series of major challenges. First of all, attacks from Javanese princes, in particular Sultan Agung of the mighty Central Javanese principality of Mataram, who wanted the Dutch out of their way. The settlers could handle that, be it with great pains. But there were other threats. The major one was the high mortality among them caused by little-known or unknown tropical diseases. Figures for those years vary between sources but 10-20 per cent of the European population died within a couple of years, often months, after arrival. Most of the survivors suffered more or less chronically from malaria, cholera, beriberi, rash and skin infections and many other diseases. Contemporary European medicine was ineffective as it did know nothing about possible causes, and thus prevention, and next to nothing about their treatment. Better ways of coping with these tropical plagues were urgently needed.

Batavia's founder and VOC governor-general Coen asked the Amsterdam office for assistance and the urgent arrival of competent medical doctors. One of them was Jacob Bontius (1592-1631), a young man who had recently graduated from the equally young University of Leiden. With not much more than fundamental knowledge of European medicine, and a book by the Portuguese physician Garcia de Orta, he arrived in 1627 in Batavia.