On 21 September, 1999, Sander went to Dili, East Timor, on a reporting mission. That same day, he was brutally murdered.

After a thorough investigation under UN flag, it has become clear that Sander has been murdered in cold blood by two officers of the Indonesian army, major Jakob Djoko Sarosa and lieutenant Camillo Dos Santos on Becora Road in Dili. Sander was executed lying on the ground, after he had fallen off the back of a taxi motorbike he was riding to visit the Becora district, where he was going to gather some quotes of people in the street. The case of the murder of Sander Thoenes is one of the many cases that has been under investigation by the UN Serious Crimes unit in East Timor. In the words of a closely involved policeman: this is a clear-cut case. Even so, a trial has up to now been effectively blocked by Indonesian pressure on the East Timor government. The murderers were never brought to justice.


- Lt Camilo dos Santos - Master of Terror
- Maj Jacob Djoko Sarosa - Master of Terror
- Serious Crimes Unit - Dili, Timor Leste
- Probe names suspect in reporter's death in East Timor (April 12, 2002)
- Hopes dim for international tribunal in Thoenes case (June 25, 2002)
- Indonesia's Choices (May 3, 2002)
- Indonesia slowly investigates Dutch journalist's death (February 15, 2002)
- A long wait for justice in East Timor (October 10, 2001)
- East Timor's avenues to justice blocked (December 27, 2000)
- E. Timor massacre suspects listed (September 5, 2000)
- East Timor general denies military wrongdoing (June 7, 2000):
- Welcome to Dili (March 17, 2000):
- A Brutal Exit (March 14, 2000):
- A Brutal Exit: Batallion 745 (March 13, 2000):
- Murder probe points to the Indonesian military (November 8, 1999):
- Indonesian military implicated (October 5, 1999):
- A dangerous obligation (September 24, 1999):
- Monitor contributor killed in East Timor (September 23, 1999):
- How Sander Thoenes Lived (September 23, 1999):