The train had arrived in Munich Hauptbahnhof (main train station) from Budapest at around 11pm on Monday, passing through Vienna, Salzburg and Rosenheim.
And in the early hours of Tuesday at 4am, the cleaners made the gruesome find.
A post-mortem has been carried out at the Institute of Forensic Medicine at Munich's Ludwig Maximilian University. Initial examinations showed the boy was killed as soon as he was born on the Railjet 68 train.
Police said in a statement, they believe the mother may have given birth to the child in the toilet cubicle.
“We still have no evidence,” a police spokesman said on Wednesday. Officers have been examining the train’s rubbish for clues.
Munich’s Abendzeitung reported on Wednesday that the baby was born between Linz and St Pölten in Austria and the case will, therefore, be taken over by Austrian police.