In a new report on Tuesday, the London-based organisation said that while systematic repression under Hussein had ended, it has been replaced by increased murders and sexual abuse - including by US forces.
Washington promised that the overthrow of the former president would free the Iraqi people from years of oppression and set them on the road to democracy.
But Amnesty said post-war insecurity had left women at risk of violence and curtailed their freedoms.
Iraqi women and girls now live in constant fear of violence, said the report.
"The lawlessness and increased killings, abductions and rapes that followed the overthrow of the government of Saddam Hussein have restricted women's freedom of movement and their ability to go to school or to work," the report said.
"Women have been subjected to sexual threats by members of the US-led forces and some women detained by US forces have been sexually abused, possibly raped."
Amnesty called on US-led forces to improve safeguards for women in detention and investigate promptly all allegations of violence against them, including sexual attacks by their forces or other agents.
The Pentagon said it had not seen the report, but took any allegations of detainee abuse seriously.
"We have demonstrated our commitment to ensuring that kind of behaviour is identified and dealt with properly," spokesman Lieutenant-Colonel Joe Richard said.
"Women have been subjected to sexual threats by members of the US-led forces and some women detained by US forces have been sexually abused, possibly raped"
"With this report, we would like the opportunity to review it and to test the validity of the allegations."
Abd al-Salam Sidahmad, director of the Middle East and North Africa Programme at Amnesty, said Iraqi authorities must now introduce concrete measures to protect women.
"They must send a clear message that violence against women will not be tolerated by investigating all allegations of abuse against women and by bringing those responsible to justice, no matter what their affiliation."
Three wars and more than a decade of economic sanctions have been particularly damaging to Iraqi women, said Amnesty.
Under Saddam Hussein's government, they were subjected to abuses such as rape and other forms of sexual violence, or targeted as political activists or as members of certain ethnic or religious groups.
And since the 2003 US-led invasion, armed groups have targeted and killed several female political leaders and women's rights activists.
Women of non-Iraqi origin have also been held as hostages, often in an attempt to force the withdrawal of foreign troops from Iraq.
Security fears are driving Iraqi
women from public life
They have been beaten and threatened with execution, and at least one of them, Margaret Hassan, was reportedly killed.
The report also said gender discrimination in Iraqi laws contributed to the persistence of violence against women.
Many women remain at risk of death or injury from male relatives if they are accused of behaviour believed to have brought dishonour on the family.
"Iraqi authorities must review discriminatory legislation against women and bring it into line with international human rights standards," said Sidahmed.
"Most importantly, they must ensure that the new constitution and all Iraqi legislation contain prohibitions to redress all forms of discrimination and gender-based violence against women."