The Honda rider has endured a bruising weekend at the German GP, crashing five times so far – the latest of which in morning warm-up left him with a fracture in his hand.
Marquez crashed in FP2 pushing for a lap time to get into Q2 and wiped out Pramac’s Johann Zarco as he exited the pitlane.
Both riders were unharmed in the incident, but locked horns as Marquez apportioned blame on Zarco.
Read more: Why the Marquez/Zarco MotoGP spat shows Honda’s situation has become untenable
Later that evening the FIM stewards issued a notification to all riders stating it was the responsibility of the competitor exiting pitlane to be aware of any oncoming traffic into Turn 1.
On Saturday, Marquez crashed three times across both qualifying sessions, leaving him seventh on the grid.
While briefly running fifth in the 15-lap sprint later that day, several early warnings on his Honda led him to backing off and he plummeted to 11th.
He later said that the risks he was taking didn’t justify the results, given the crashes he had already had.
On Sunday morning in the 10-minute warm-up session, Marquez suffered his fifth crash of the Germany weekend when he was flicked from his Honda going through Turn 6.
Marquez was later diagnosed with a small fracture in his hand and told Spanish television that he would evaluate his continued participation at the Sachsenring in the coming hours.
A brief statement from Honda gave no other details on his decision, other than “Marc Marquez has elected to miss the German Grand Prix after suffering a crash at Turn 7 during morning warm-up.
Speaking to DAZN after withdrawing, Marquez said: "After four or five crashes, especially the one this morning, well, I don't feel ready to race, to do the race. And I decided 'calm down'... and in Netherlands even more."
"I don't feel ready. I have many bumps in my body, especially in my ankle, a fracture [to my hand]... I don't feel ready."
Prior to Saturday’s sprint race, Marquez had won every race he had entered at the Sachsenring since the 2010 125cc grand prix.
With the Dutch GP following next weekend and all of the problems Marquez has faced on the Honda in Germany, it is unclear at this stage if he will contest the Assen round.
Marquez’s withdrawal from the German GP means just one Honda rider will be present in the race in the form of LCR’s Takaaki Nakagami, with Joan Mir suffering a hand fracture and Alex Rins a broken leg in separate crashes at Mugello.