Von Wernich was arrested in 2003, after the Constitutional Court had declared as being unconstitutional the Amnesty Law (“Ley de Punto Final”) and the Due Obedience Law (“Ley de Obediencia debida”).
He was put under investigation in two different criminal procedures, both of which were conducted by Judge Arnaldo Corazza from la Plata.
In 2003, as part of the first procedure, he was put under preventive detention for his possible involvement in 33 arbitrary detentions and 19 arbitrary killings.
On 29 December 2005, as part of the second procedure, judge Corazza also arraigned him on charges concerning 20 other cases of serious human rights violations: 12 cases of arbitrary detention and 8 cases of torture in the clandestine detention centres of "Puesto Vasco", "Destacamento de Arana", "Coti Martinez" and "Pozo de Quilmes". This later process became known as "Camps II", in the course of which several other persons were also to be investigated and detained.
The judge held that von Wernich’s visits to the detention centres “formed part of a devastating machinery aimed at the violation of the personal liberty and the humiliation of the persons who were illegally detained”.
The trial before the tribunal in La Plata (Argentina) began on 5 July 2007. Von Wernich denied all charges against him and refused to appear before the tribunal.
On 16 October 2007 an Argentine tribunal sentenced von Wernich to life imprisonment. He was found guilty of involvement in seven murders, 31 cases of torture and 42 kidnappings. He became the first Catholic priest to be prosecuted in connection with human rights violations in Argentina.