Definitely check out the mosque and university of Al Azhar. Al Azhar is the oldest Islamic university of the Islamic world, and a beautiful building.
The market of Khan Khalili is great to visit, but closed certain days, so try and find out when. It's got lots of different things; be sure not to get cornered by sales people. If you wander far beyond the main strip, you'll find a local Cairene food market and its fascinating to walk through it, really lots of fun.
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The Islamic part is open every day and, in general, the touristic part of Khan El Khalili is open from the morning until late in the evening every day of the week.