Officers have been searching Brimham Rocks, near Knaresborough, in the wake of the arrest of a man who has admitted killing Miss Simpson.
She was 23 when she vanished in May 2000 after telling a friend she was catching a bus from her home in Harehills to Leeds city centre.
Last night Detective Chief Inspector Adrian Taylor, of West Yorkshire Police, said: “Officers investigating the murder of Gemma Simpson can now confirm that human remains located in the vicinity of Brimham Rocks in North Yorkshire are those of Gemma.
“Gemma’s family have been informed.”
Martin Bell, 43, of St Leonard’s Crescent, Scarborough, was last month charged with her murder at a flat in Knaresborough Road, Harrogate, between May 4 and June 3, 2000.