Egypt's main index slumped to a two-week low on Sunday following violence at a protest by thousands of Egyptians demanding that ousted President Hosni Mubarak and former officials be put on trial.
Other Middle East benchmarks were broadly upbeat as rising oil prices and expectations of improved quarterly earnings boosted sentiment.
Cairo's index fell 1.4 percent, its lowest finish since March 28.
Soldiers and police used electroshock tasers and batons to try to drive protesters from Tahrir Square on Friday, but more than 1,000 defied the move and stayed. Sources said 13 men were wounded by gunfire and two died in Egypt's biggest rally since February 18.
All but two of the 30 stocks on the index fell, with Egyptian Resorts dropping 7.9 percent and real estate developer Palm Hills declining 2.8percent.
Private equity firm Citadel Capital rose 2.3 percent. ASEC Company for Mining, 39-percent owned by Citadel, has discovered large gold reserves in an area near the border between Ethiopia and Sudan, newspaper Al Ahram reported.
Dubai's index rose 0.9 percent to a seven-week high as Dubai Investment Co climbed 2.9 percent and Emaar Properties rose 1.3 percent.
"We are seeing interest returning to the UAE as a safe haven from regional turmoil - people are also accumulating positions ahead of a possible MSCI upgrade," said Matthew Wakeman, EFG-Hermes managing director for cash and equity trading.
Index compiler MSCI will announce in June whether it will raise the UAE and Qatar bourses to emerging markets.
Both countries are currently rated as frontier markets, but have failed to meet key requirements to be upgraded, while low trading volumes and regional unrest are also dampening prospects, some traders said.
"Investors expect Q1 earnings to be okay and UAE stocks are pretty good value compared to elsewhere in the region," said Wakeman. "Sentiment towards the UAE has changed a lot over the past few months."
Local and foreign investors are buying UAE stocks, he added, but property and bank results will determine whether markets can mount a sustained rally, with these sectors dominant.
Saudi Arabia's Riyad Bank fell 1.1 percent. The bank, the kingdom's third largest by market value, reported an 8.3 percent rise in first-quarter profit following improved income from banking services.
"Geopolitical events have hindered banks - many people or companies that wanted to borrow money were scared by what was happening in the region and so lending was limited in Q1," said Youssef Kassantini, a Saudi-based financial analyst.
"I expect banks to do very well for the rest of the year because of strong government spending, while banks have taken full provisions for 2010 and now have extra cash to lend. Consumer confidence will slowly improve."
Other bank stocks declined. Al-Rajhi Bank and SABB each slid 1.3 percent.
Saudi Arabia's king has announced about $130 billion in extra state social spending in the wake of deadly unrest in neighbouring Bahrain and Oman.