Heavyweight stocks dragged Egypt's index down 0.3 percent to 5,508 points, but talk of a possible takeover bid for private equity company Citadel Capital lifted sentiment.
Abu Dhabi's index rose 1 percent to a three-week high and Dubai's index rose 0.9 percent to 1,574 points, its fourth gain in five sessions.
Property and construction stocks dominated trading, with Emaar Properties climbing 1.6 percent and Arabtec gaining 0.7 percent.
World stocks hovered at three-week highs and the euro neared a one-month peak on Wednesday as investors hoped for progress in an aid package for Greece that would ease fears of a default by Athens.
"We're positive across the region because globally stocks did well yesterday (Tuesday) - with the exception of Qatar on MSCI uncertainty," said Shahid Hameed, Global Investment House head of asset management for the Gulf region.
Investors are increasingly doubting Qatar will be included in MCSI's emerging market index after the Doha exchange said on Monday it would not be lifting the foreign ownership limit from 25 percent this year.
"This decision will have a negative effect on the market," said Hani Girgis, assistant chief dealer at Dlala brokerage.
"We don't think Qatar can be included in the MSCI (without an increase in the foreign ownership limit)."
Doha's benchmark slipped 0.6 percent to 8,327 points, tumbling to its lowest close since March 24.
Losers outnumbered gainers 15 to four. Volumes in Vodafone Qatar hit a month-high as the stock fell 1.3 percent after Nomura cut its share-price target for the telco.
In Saudi Arabia, the Tadawul All-Share Index (TASI) edged up 0.09 percent to 6,742 points. The value of Saudi traded shares reached SR5.77 billion on Wednesday.
In Egypt, Commercial International Bank (CIB) dipped 2 percent, EFG Hermes dell 1.4 percent and Orascom Telecom shed 0.9 percent.
"Heavyweights are pulling back a bit and they're weighing on the overall market," said Hashem Ghoneim, vice chairman of Pyramids Capital. "They've had a good run, so it's normal they slow down."
Citadel Capital closed up 0.3 percent despite posting a net loss of $241.7 million in 2010 due to writedowns, having gained as much as 8 percent earlier in the day, following market talk that a Dubai-based firm may be eyeing Citadel.
Oman's Bank Muscat, the sultanate's top lender by value, extended gains since Bank of America Merrill Lynch upgraded its rating for the stock to “buy”. Its shares rose 4.6 percent to 0.754 rials — its largest gain since April 3.
Loan growth at Bank Muscat will likely gain momentum this year, driven by a pick-up in corporate credit activity, the US bank wrote in a note, raising its price target to 0.960 rials from 0.920 rial.
Oman's index rose for a third day since Sunday's 22-month low, climbing 1.1 percent.
Blue chip Renaissance Services jumped 4 percent, trimming its 2011 losses to 21 percent to 6,075 points.
The Kuwaiti measure climbed 0.2 percent to 6,390 points.
The Bahraini index eased 0.2 percent to 1,349 points.