Thomas Mair, 53, allegedly shot and stabbed the 41-year-old outside her constituency surgery in Birstall, near Leeds, on June 16 this year.
He is charged with Mrs Cox’s murder, possession of a firearm with intent to commit an indictable offence and possession of an offensive weapon – a dagger.
He is also charged with causing grievous bodily harm with intent to Bernard Carter-Kenny on the same date.
Mair, from Birstall, has been in custody since the day Mrs Cox was killed on June 16 and his case is being treated under the “terrorism protocol”.
Cases such as this are managed by senior judges, usually sitting at the Old Bailey.
Mrs Cox’s sister was among family members who gathered at the Old Bailey for the short hearing yesterday morning.
Wearing red trousers and a white sweatshirt, the bearded defendant appeared at the court in central London via a live video link from Belmarsh prison before senior judge Mr Justice Wilkie.
He spoke to confirm his name and then sat with his arms crossed and stayed silent as he was asked to enter pleas. He confirmed, when asked, that he could hear the charges being put to him by court staff.
The judge ordered, in light of his silence, that not guilty pleas be entered on all the charges.
A provisional four-week trial date has already been fixed for November 14. The judge adjourned the case to a further hearing on October 28 and remanded Mair in custody.
During a hearing in September, Tom Little, for the prosecution, told the court that Mair would not be relying on medical evidence when he went on trial.
The accused made his first crown court appearance In June before Mr Justice Sweeney via video link from top security Belmarsh prison. During that brief hearing, he spoke only to confirm his name.
Mrs Cox, a mother-of-two, was attacked during the European Union referendum campaign. She had only been elected as an MP in May last year.
She had spent the morning of June 16 visiting a school and a care home in her constituency and was on her way to a meeting with constituents when she was killed.
At the time of her death, Mrs Cox was described by Labour leader Jeremy Corbyn as “one of our very best”.
She left a husband, Brendan, and two young children, who were aged three and five when their mother died.
Prior to entering politics, she held roles including head of policy and advocacy at the charity Oxfam GB.
She was selected to contest the Batley and Spen parliamentary seat after the previous incumbent decided not to stand in 2015.
Mrs Cox’s family divided their time between their constituency home and a houseboat, a converted Dutch barge, on the Thames in London.
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