UN human rights investigators say the Syrian government is using what they call "enforced disappearances" as part of a widespread campaign of terror against civilians.
Thousands of people have been taken away, with most never seen again, their report says.
It notes that some opposition groups have begun taking hostages - which also constitutes a human rights violation.
Rebel groups such as the al-Qaida-linked Islamic State in Iraq and the Levant have begun seizing people and running secret prisons.
The evidence in this report comes from former officers in the Syrian army who have defected - and from families of those who have gone missing.
"Enforced disappearances are perpetrated as part of a widespread campaign of terror against the civilian population," says the study by the Independent International Commission of Inquiry on the Syrian Arab Republic.
"There are reasonable grounds to believe that enforced disappearances were committed by government forces, as part of a widespread and systematic attack against the civilian population, and therefore amount to a crime against humanity."
Many families of the disappeared are afraid to ask about their whereabouts, the investigators add.
The BBC's Imogen Foulkes in Geneva says the report talks of a clear pattern emerging in the use of enforced disappearances.
At the start of the conflict, young men taking part in anti-government demonstrations were systematically arrested - never to be seen again.
Since then, the net has widened, with mass arrests and targeted detentions of people such as civilians living in opposition areas and medical staff treating the wounded.
A few families have had bodies of their relatives returned to them - bearing obvious signs of torture. Often no information was provided about the grounds for detention or the circumstances of the deaths.
More than 100,000 people are estimated to have been killed in the conflict in Syria.
More than two million Syrians have fled the country - around half of those are believed to be children.