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Scott Lively denies helping anti-gay groups in Uganda spread violence against gays.
He told the BBC the case was based on “gross misrepresentations” and should not be actionable.
Sexual Ministries Uganda is seeking a judgement against Mr Lively and unspecified damages.
“We hope that he will be held accountable for what he did in Uganda,” Frank Mugisha, head of the group, told the Associated Press news agency.
The Center for Constitutional Rights (CCR) filed the complaint on behalf of Sexual Ministries Uganda in a federal court in Massachusetts, where Mr Lively is based.
The case is based on a statute they say allows foreigners to file civil lawsuits against Americans for alleged violations of international law.
To mark the legal action, about 70 protesters marched from the US district court in Springfield, Massachusetts on Wednesday.
Mr Lively was one of several US evangelicals who visited Uganda in 2009 shortly before a bill was drafted that made certain homosexual acts punishable by death.
That bill has since been amended with a life prison sentence instead of the death penalty, but gay groups in Uganda say they have faced increasing threats since its introduction.
Mr Lively, who leads Abiding Truth Ministries, said he never told the Ugandan legislature to implement the death penalty and has informed them he disapproved of the punishment.
He said he believed “in criminalisation in the same manner of criminalisation of marijuana and speeding on the highway”.
“This is just political theatre,” Mr Lively told the BBC, arguing that the case is a frivolous one based on highly edited comments that misrepresent him.
The complaint alleges Mr Lively warned Ugandans to fight against a “genocidal” and “paedophilic” gay movement, “which he likened to the Nazis and Rwandan murderers”.
Sexual Ministries Uganda’s complaint also alleges that Mr Lively’s involvement in Uganda’s anti-gay movement stretches back to 2002.
“He long ago set out a very specific and detailed methodology for stripping away the most basic human rights protections, to silence and ultimately disappear LGBT people,” Pam Spees, an attorney with the Center for Constitutional Rights, said in a statement.
“Unfortunately, he found willing accomplices and fertile ground in Uganda.”
Some have argued that the anti-gay bill is part of an effort to distract Ugandans from government corruption.