Offensive material was left inside books at The Trafford Centre branch of Waterstones.
The transphobic leaflets were found inside gender identity books bought by customers last week.
Book shop bosses shared details of the incident on social media and said that hate would not be tolerated at its stores, threatening to ban anyone caught distributing the leaflets and apologising to anyone who had been affected.
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It's not known exactly what was said on the leaflets, but the nature of the content and where they were left, made it clear it was a deliberate attempt to target those people reading such material.
In a tweet posted on March 2, which has since been deleted, the Waterstones Trafford page wrote: "It has come to our attention that some transphobic materials have been left in some of our Queer Identity books. If you are found to be doing this you will be banned from our store. We do not condone any form of hate spreading.
"If you have bought anything from that section over the last week or so we whole heartedly apologise if you find any of these materials. We try hard to make our shop a safe space and will continue to do so in the face of this."
A spokesperson for Waterstones added: "We confirm that someone left flyers in our Trafford Centre bookshop last week. Our booksellers removed the material as soon as it was found. We do not tolerate leafleting in our shops and especially regret this when the content is objectionable."
The Trafford Centre's Waterstones store is on the ground floor of the mall, in Peel Avenue, close to John Lewis.
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