Thomas Mair, 53, is accused of shooting and stabbing Labour MP Mrs Cox, 41, outside Birstall Library on June 16.
He refused to speak when asked to enter pleas at the Old Bailey during a hearing this morning.
Jo Cox case: Live blog
Mair, of Lowood Lane, Birstall, has been held in custody since his arrest on the day Mrs Cox was killed.
He is charged with murder, grievous bodily harm, possession of a firearm with intent to commit an indictable offence and possession of an offensive weapon – a dagger.
The case is being handled under the “terrorism protocol” as part of a terror list.
Wearing red trousers and a white sweatshirt, the bearded defendant appeared via 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.
The judge ordered, in light of his silence, that not guilty pleas be entered on all the charges.
Members of Mrs Cox’s family gathered at the Old Bailey to see Mair in court.
A provisional four-week trial date has already been fixed for November 14.
The judge adjourned the case for a further hearing on October 28.
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