The rights group said detainees held by the Islamic State of Iraq and the Levant (ISIL) include children as young as eight and that minors have been sentenced to severe floggings and held with adults in "cruel and inhuman conditions".
It described individuals being seized by masked men, held for weeks on end in solitary confinement at unknown locations and tried by self-styled religious courts that mete out death or floggings with little if any due process.
Former detainees described being beaten with rubber generator belts or cables, tortured with electric shocks and being forced into a painful stress position known as the "scorpion" in which the detainee's wrists are bound over one shoulder.
"After years in which they were prey to the brutality of (President Bashar al-Assad's) regime, the people of Raqa and Aleppo are now suffering under a new form of tyranny imposed on them by (ISIL), in which arbitrary detention, torture and executions have become the order of the day," said Philip Luther, Amnesty's director for the Middle East and North Africa.
Amnesty said some people are detained for common crimes like theft while others are jailed for smoking, sex outside of marriage, or because they challenged ISIL's rule or belong to other armed groups.
In recent months, ISIL has kidnapped dozens of Syrian activists and news providers, as well as several foreign journalists.
Amnesty described one sharia court near a dam on the Euphrates river where a judge had instituted a "reign of terror," saying he invariably wore an explosives belt to trials and meted out punishments within minutes.
On at least one occasion he was said to have personally joined the flogging of a detainee.
Amnesty said two 14-year-olds were among those sentenced to floggings, and described how one father was forced to listen to his son's screams of pain as he was tortured in a nearby room.
The rights group called on Turkey and Gulf states - which support mainstream rebel groups - to take measures to prevent the flow of arms and aid to ISIL and other groups accused of human rights violations.
Assad's regime has long been accused of torturing and killing detainees, and this week Britain accused the government of having "in effect murdered" a British doctor who was seized in Aleppo by regime forces and died in detention.
ISIL is the latest incarnation of al Qaeda's Iraqi affiliate, and has carried out scores of suicide bombings and other attacks in both Syria and Iraq.
It is believed to include large numbers of foreign fighters and aims to create an Islamic state that would supercede national borders.
An estimated 126,000 people have been killed since the start of the Syrian uprising, which began as a series of pro-democracy protests in March 2011 but escalated into a civil war following a brutal regime crackdown.
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There will definitely be a Pakistani connection to this too.