Among the items was a uniform thought to have belonged to a Polish baker who died in Auschwitz, which was on sale for £11,200, according to an investigation by a Sunday tabloid newspaper.
The site apologised and said it had made a donation of £25,000 to charity.
Other items reported to be for sale included shoes and a toothbrush belonging to a death camp victim and Star of David armbands used to mark out Jews for persecution.
A spokesman said the items had been removed "in view of the seriousness of the issue".
It said in a statement: "We are very sorry that these items have been listed on eBay and we are removing them.
"We don't allow listings of this nature, and dedicate thousands of staff to policing our site and use the latest technology to detect items that shouldn't be for sale."