Cairo's main index fell 1.3 percent to 4,247 points, weighed by Orascom Construction (OCI) which dropped 4.6 percent to its lowest level since March.
"Everybody is really bearish especially because of what may happen next Friday," said Omar Ascar of Cairo Capital Securities, referring to calls for protests on Friday.
In Saudi Arabia, the Tadawul All-Share Index (TASI) rose 0.4 percent to 6,128.47, up for a second day, as sharp gains in world markets boosted sentiment.
Petrochemical stocks led by turnover, with the sector index climbing 0.6 percent. Bellwether Saudi Basic Industries Corp. (SABIC) rose 0.5 percent.
Investors booked profit in insurance stocks, the focus of the last few sessions. The sector index dropped 2.4 percent from Monday's 10-week high.
Agriculture stocks also rose and were among the most active. Investors often target sectors that rely on local, rather than international demand, when global markets are volatile.
Food Products gained 4.2 percent and Sharqiya Development Co. climbed 3.7 percent.
"(Buying) domestic driven stocks is the best strategy going forward, and maybe keep petchems on the side because they are ridiculously cheap,” said Haissam Arabi, chief executive and fund manager at Gulfmena Investments.
Elsewhere, Aluminium Bahrain slumped to an all-time low, extending losses for a fourth day since saying the government would raise natural gas prices from 2012 in a subsidy-slashing move.
Bahrain's index fell 1.6 percent to 1,200 points — its lowest level since September 2003.
Analysts say weak volumes are troubling the market, with Aluminium Bahrain causing an additional drag.
Qatar's index rose 0.4 percent to 8,418 points, Abu Dhabi gained 0.5 percent to 2,544 points and Dubai climbed 0.1 percent to 1,448 points, lifted by gains in global markets.
"Our markets have held up quite well given the uncertainties in Europe and US, that's an encouraging sign and makes me think we're forming a bottom here in UAE and Qatar," said Tarek Lotfy, Arqaam Capital head of MENA equities.
In Kuwait, the index fell 0.4 percent to 5,854 points as investors booked profits from Monday's rally.
"Everyone is getting rid of their positions because no one is positive in the market," said a Kuwait-based fund manager on condition of anonymity. "It is not a good place to invest now days... because of volumes."
Burgan Co. for Well Drilling, resuming trade since last trading on Aug. 15, jumped 8.5 percent after saying it won a $173.5 million oil well drilling deal from Kuwait Gulf Oil Co.
Kuwait bourse employees agreed to give authorities three weeks to meet their demands, delaying a planned strike which could affect trading on the second largest Arab market.
The Omani index edged up 0.09 percent to 5,647 points.
