The protest near Istanbul's Blue Mosque and the Haghia Sofia mosque was peaceful. Police kept demonstrators away from the site where athletes planned to begin running with the torch through the city.
The Olympic flame is on a global tour before the games begin in Beijing.
Uighurs are related to Turks, and Turkey is home to a Uighur community.
"Turkey, stand by your brothers," read a banner at the protest in Istanbul.
"We don't want a country like China, with a bad human rights record, to hold the Olympics, which symbolize humanity, peace and brotherhood," protester Hayrullah Efendigil said.
Police outnumbered the protesters and hemmed them in, making it difficult for them to move around freely. Some tourists photographed the group.
Uighur Muslims have been calling for independence for East Turkistan.
Last Mod: 03 Nisan 2008, 16:45
In the late 1990s, the Chinese leadership exerted a lot of pressure on Turkey to silence and withdraw any government support for these advocates.