Thomas Mair, 53, allegedly shot and stabbed Mrs Cox, 41, outside her constituency surgery in Birstall, near Leeds, on June 16.
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.
Mair, from Birstall, is in custody and his case is being treated under the “terrorism protocol”.
Wearing red trousers and a white sweatshirt, the bearded defendant appeared via video- link from Belmarsh prison before senior judge Mr Justice Wilkie.
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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.
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.