His lawyer, Guenter Maull, said the suspect had sat in a chair while the 21-page warrant was read and translated into his native Ukrainian language.
Mr Demjanjuk "showed no emotion, with few facial movements" but had understood the charges, he said.
He denies accusations that he worked as a guard in the Sobibor Nazi death camp in Poland during World War II.
Mr Demjanjuk, who settled in the US in 1952, says he was captured by the Germans in his native Ukraine during the war and kept as a prisoner of war.
'In good shape'
He is being kept under medical observation to allow experts to determine whether he is fit to go to trial - an assessment which may take weeks.
US government surveillance video showing John Demjanjuk walking without help
But deputy prison director Jochen Menzel said Mr Demjanjuk was in strikingly good condition.
"He is not typical for his age... he is in better shape than usual for an 89-year-old," he told German news channel N24.
His lawyers had argued in US courts that he was too frail to be deported, but the US government, which secretly shot footage showing him walking without assistance, argued he was fit to travel.
An appeals court ruled against him, saying it was satisfied that he would be provided with adequate care.
STADELHEIM PRISON, MUNICH
Largest in Bavaria, maximum of 1600 prisoners
Built in 1804, Hitler detained there in summer 1922
Demjanjuk shares cell with one other inmate in prison hospital
20 sqm (215sq ft) cell has basin and toilet, shower facility on same floor
Mr Demjanjuk arrived in the US in 1952 as a refugee, settling in Cleveland, Ohio, where he worked in the car industry.
In 1988 he was sentenced to death in Israel for crimes against humanity, after Holocaust survivors identified him as a notorious guard at the Treblinka death camp. But the Israeli Supreme Court overturned that conviction and he returned to the US.
Prosecutors now say they have documents which prove his Nazi background, including an SS identity card which shows he was posted to the death camp in Sobibor in 1943, and many witness testimonies.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.