The high-street retailer, which also sells unisex childrenswear collections, wants parents and children to have a wider choice in what they wear.
The labels on the clothing now read: “Girls & Boys” or “Boys & Girls”.
“At John Lewis, ensuring we meet our customer needs is our number one priority,” said Caroline Bettis, head of childrenswear at John Lewis.
“As such, we introduced new non-gender specific John Lewis stitched labels and combined ‘Girls & Boys’ swing tags to clothing for John Lewis own label collections in 2016.
“In line with this change, our policy is to no longer specify areas or use signage which say ‘Girls’ or ‘Boys’ in our shops.”
Bettis added: “We do not want to reinforce gender stereotypes within our John Lewis collections and instead want to provide greater choice and variety to our customers, so that the parent or child can choose what they would like to wear.”
The John Lewis website still has separate sections for girls and boys, but this is expected to be reviewed.
Reactions to the gender-neutral label and signage in the stores has been mixed. Some felt the move was positive.
A campaign for gender-neutral clothes, Let Clothes Be Clothes, said they were “absolutely thrilled” by the announcement and many Twitter users also expressed how pleased they were online.
However other people disagreed with the move - Piers Morgan being one of those. He said on ‘Good Morning Britain’ on Monday 4 September: “I have three sons and one little daughter.
“None of my sons have shown any interest in wearing dresses, and my daughter wears 20 dresses a day. Why can’t we let boys be boys and girls be girls?”
Others felt ditching the labels was “worrying”.