Allegations of torture have regularly emerged since the US-led invasion
Routine torture, including electric shocks and sexual abuse, was inflicted on detainees held in a secret prison in Baghdad, Human Rights Watch says.
The group's findings are based on interviews with more than 40 people, including a British man who said Iraqi army interrogators were responsible.
Human Rights Watch says the men's stories are credible and consistent.
The Iraqi authorities deny operating secret detention centres, but there have been past allegations of abuse.
In 2006, the UN's special rapporteur on torture said the situation was "out of control" and might be worse than under Saddam Hussein.
More than 400 prisoners were said to have been held at the secret detention centre at an airbase in Baghdad.
One of the prisoners, a 68-year-old man with dual British and Iraqi citizenship, said he had been harshly beaten, sodomised and had electric current passed through his genitals.
Human Rights Watch said he and his fellow detainees were accused of aiding and abetting terrorism, though no-one was officially charged.
The BBC has spoken to a number of other men who were released from the same detention centre and they tell similar stories.
"The torture started when they put plastic bags over our heads. Then they tortured us with electric shocks after pouring water over our bodies," one man said.
The detention centre has now been closed. Some of the detainees have been released, though the majority have been moved to a different prison.
The Iraqi government denies that it operates secret detention centres, or that abuse in its jails is endemic.
Human Rights Watch, though, called the evidence "credible and consistent", the torture "routine and systematic".
The British embassy in Baghdad said it was aware of a British-Iraqi national being detained in Iraq and that consular officials had visited him in prison and were providing him with assistance.