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.

Thieves broke into the house in Intake, Doncaster on Thursday, a week after Paris Mulholland's 11th birthday.
In the letter, she tells the burglars "how much they hurt me", that she cries for two hours each night, and they had made her "scared of the dark again".
Paris wrote the letter after speaking to BBC Radio Sheffield.
More on this and other stories from BBC South Yorkshire
Gemma Mulholland said the letter helped her daughter tell the thieves "how she feels, and how it's affected her."
She said: "I really am super proud of her."
Paris' new iPhone, a laptop she got for Christmas, and birthday money was taken from her bedroom, as well as her grandmother's gold watch.
Cash, jewellery and other items were taken in the robbery, along with Paris' and her younger brother Thomas' belongings.
Ms Mulholland said Paris was too upset to sleep in her bedroom after seeing it ransacked.
Lego models were broken and photos taken on Paris' phone during a recent trip to Disneyland may have been lost forever.
Paris wrote: "To my burgler [sic]. I hope you are happy with yourself, I can no longer sleep in my own bed [...]
"Why could you not have left when you saw to [sic] picture of a happy family and when you saw my birthday card, but anyway thank you for scaring me so much I cry 2 hours straight nearly every night."
Ms Mulholland called the thieves "despicable human beings" but said the community had rallied round.
PC Adam Watkinson of South Yorkshire Police said: "Burglary is a highly intrusive crime which can have a huge impact on the victim. In this case, a young girl has been left feeling scared and upset after her home was broken into.
"I would like to reassure Paris and her mum that we are doing everything we can to find the person responsible for this incident.
"It is totally unacceptable that someone should feel scared in their own home and lose valuable possessions."

South Wales Police said 39-year-old Angharad Bullock was reported missing on 28 April, along with the toddler.
Officers are concerned for the welfare of the pair.
The prosecution has rested its case in the trial of a man accused of carrying out the 2013 Boston Marathon bombings.
[NEXT_CONCEPT]
An 11-year-old girl has written a letter to burglars who raided her home and stole birthday and Christmas presents.
[NEXT_CONCEPT]
Police are searching for a woman who has gone missing with her three-year-old son.