The war crimes tribunal accused Delawar Hossain Sayedee of mass murder and torture among other crimes. He denies all the allegations.
Mr Sayedee, a leader in Bangladesh's Jamaat-e-Islami party, was arrested last year.
The tribunal was set up in 2010 to try those accused of crimes during the war.
Bangladesh was called East Pakistan until 1971 when a nine-month war of secession broke out leaving up to three million people dead.
"The court has framed charges on 20 counts including crimes against humanity and genocide against Mr Sayedee," Mohammad Shahinur Islam, registrar of the International Crimes Tribunal, told the BBC.
"He pleaded not guilty. He claimed all those allegations were false.
"With the framing of charges the trial has started. As a citizen, I should say this is a historic day for Bangladesh," Mr Islam said.
The case will be next heard on 30 October when the prosecution will make an opening statement.
Official figures estimate that thousands of women were raped when West Pakistan sent in its army to try and stop East Pakistan becoming an independent Bangladesh.
Last year, the Bangladeshi government set up the International Crimes Tribunal in Dhaka to try those Bangladeshis accused of collaborating with Pakistani forces and committing atrocities during months of violence.
Mr Sayedee is among seven people, including two from the main opposition Bangladeshi Nationalist Party, facing trial. All of them deny the accusations and accuse the government of carrying out a vendetta.
The New York-based Human Rights Watch says the tribunal needs to change some of its procedures to ensure a fair trial which meets international standards.
The trial is likely to go on for months.
A senior leader of Bangladesh's largest Islamic party is the first suspect charged by a tribunal probing the 1971 independence struggle against Pakistan.