Dzhokhar Tsarnaev, 21, is charged with 30 counts related to the bombings, which killed three people and wounded more than 260 in April 2013.
As part of the prosecution's summing up, medical examiners gave graphic details of the injuries suffered by those who died in the attack.
Mr Tsarnaev could face the death penalty if found guilty.
Massachusetts Chief Medical Examiner Henry Nields testified that the youngest victim of the attacks, eight-year-old Martin Richard, received injuries to every part of his body.
The testimony was illustrated by autopsy photos and the child's bloody, torn clothing.
Mr Nields said one piece of shrapnel appeared to have gone straight through Richard's body.
"It would be difficult to say the precise location due to the size of the openings in the abdomen," he testified, according to Reuters.
The defence began calling its own witnesses later on Monday.
Earlier in the trial, the defence made the surprise admission that Mr Tsarnaev had participated in the attacks.
But defence lawyers argue that his 26-year-old brother, Tamerlan, had been the driving force behind the attacks. By doing so they hope to spare their client the death penalty.
Mr Tsarnaev is charged with 30 counts related to the bombings. The brothers set off a pair of homemade pressure-cooker bombs at the race's crowded finish line.
Mr Tsarnaev is also accused of fatally shooting a police officer three days later.
The prosecution says Mr Tsarnaev, who emigrated with his family from Chechnya, had extremist views and wanted to hit back at the US in revenge for military action in Muslim countries.
The prosecution has rested its case in the trial of a man accused of carrying out the 2013 Boston Marathon bombings.