Many Uighurs resent the large-scale influx of Han Chinese settlers into resource-rich Xinjiang. There is periodic violence attributed to groups seeking an independent Islamic nation.
Beijing accuses these groups of links to al-Qaeda and says it has uncovered a number of Xinjiang-based plots targeting the Olympic Games.
But human rights groups say China uses the alleged terror links as a way of cracking down on the independence movement.
Kashgar is seen as one of the main Islamic centres in the region - more so than Urumqi, where Tuesday's relay passed off peacefully.
The relay in Kashgar began at the main square in front of the city's giant Idkhar Mosque.
The BBC's James Reynolds, in Kashgar, said that there was a huge security presence, with police searching people thoroughly.
We saw sizeable but very carefully chosen crowds on both sides of the road
As in Urumqi, some residents told the BBC they had been told to stay at home and watch the relay on television.
A short ceremony was held in the square and then the first runner ran out on a red carpet in front of a carefully-selected cheering crowd, our correspondent said.
After the torch's run through the Silk Road oasis city of Kashgar, it moves on to the cities of Shihezi and Changji on Thursday.
Are you in Urumqi or Kashgar? Did you witness the torch relay in Urumqi? Will you be attending the procession in Kashgar? Send us your comments and experiences.
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