The INAA contested 17 parliament seats and 23 of 40 municipal seats.
About 295,000 voters were entitled to elect 39 MPs in an equal number of constituencies. There are a total of 206 candidates, including 17 women. Turnout reached 72 per cent.
One seat in the 40-strong chamber has already gone to Latifa al-Quhud, who stood unopposed in her constituency, making her the first woman MP in the Gulf state's history.
Sheikh Ali Salman, the leader of the Islamic National Accord Association (INAA) and a candidate in the mostly Shia northern town of Jid Hafas, had criticised the conduct of the election saying "there should be more ballot boxes".
"There should be more ballot boxes"
Sheikh Ali Salman, the leader of the Islamic National Accord Association
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However, he said that the high turnout "proves the popularity" of the INAA, the main Shia opposition group.
During the election, the group allied itself with Sunni liberals and left-of-centre candidates.
Like the Shias, they boycotted the last legislative elections in 2002 in protest at the split of legislative powers between parliament and an equally numbered upper chamber appointed by the king, which can block parliamentary initiatives.
Many Shias accuse the government of plotting to maintain pro-government Sunni domination of the tiny kingdom, mainly through naturalised Bahrainis, including those coming from Saudi Arabia across the causeway linking the two countries.
The causeway's public voting centre is one of 10 out-of-constituency ballot stations that the opposition had demanded be shut.
Several Saudi registered cars were seen parked outside the polling station, and an INAA representative at the centre said many dual citizens came from Saudi Arabia just to vote.
On Friday, about 2,000 demonstrators called for an investigation into an alleged plot aimed at marginalising the Shia majority, and demanded the resignation of Sheikh Khalifa bin Salman al-Khalifa, the country's long-serving prime minister.