The Israeli court extended the 18-year-old's remand at the hearing in Rishon Lezion, near Tel Aviv.
The Israeli court extended the 18-year-old's remand at the hearing in Rishon Lezion, near Tel Aviv, to April 6 following the Jewish teenager's arrest in the southern Israeli city of Ashkelon on March 23.
His father, also arrested as part of the investigation, was released as the probe that has involved the FBI continues.
A gag order prevents their identities from being published.
Their arrests followed a wave of bomb threats to American Jewish institutions since the start of the year, which helped spread fears over whether hate crimes and anti-Semitic acts have been on the increase in the country.
Some have said that the rise of Donald Trump as US president has encouraged the extreme right and emboldened hate groups.
The arrest of a Jewish teenager over dozens of the threats has however complicated the debate.
His alleged motive is unclear, but his lawyer, Shira Nir, highlighted his medical condition, which she said may have led him to wrongdoing through no fault of his own.
She showed the court an image of what appeared to be a tumour on the right side of his brain, but gave no medical details.
"The tumour is in a place where it's very dangerous to operate," she told the court, while also saying he suffered from autism.
She said he had fallen asleep at one point as police questioned him and officers handled him roughly, resulting in bruises on his face.
Turning down Nir's request that he be moved to house arrest under his mother's supervision, judge Amit Michles said that the accused was suspected of carrying out offences "for years while his parents were in the home."
As he was being led out of court, his legs shackled, he stumbled and his mother burst into tears at the back of the room.
The judge ordered police to provide the prison service with his medical records after Nir said guards had not been made aware of his condition.
The suspect is a dual US-Israeli citizen.
Police say he is behind a range of threats against Jewish community centres and other buildings linked to Jewish communities in the United States in recent months.
The teenager is also suspected of being behind similar threats in New Zealand and Australia.
In addition, police say he is suspected of a bomb threat to Delta Airlines in February 2015 which led to an emergency landing.
Police said he used voice-disguising technology when making calls. Authorities have seized computer equipment and other items.