Rights groups have accused the authorities of widespread abuses of the electoral system since voting began on 9 November, including blocking access for voters to polling stations, vote-buying and fabricating results.
The Muslim Brotherhood has won 76 seats in the 454-seat People's Assembly, confirming its status as Egypt's biggest opposition group.
The officially banned group was given unexpected leeway to run but says its gains have prompted a crackdown. It says more than 1500 of its members have been detained since voting started.
Brotherhood spokesman Badr Mohamed Badr said that the crackdown was intended to scare voters and that some arrests were "a type of revenge on those governorates which stood by the Brotherhood".
The Brotherhood and some rights groups have accused the United States, Egypt's biggest aid donor, of ignoring electoral abuses.
Washington has urged its Middle East ally to ensure a clean race.
Violence broke out in earlier
rounds of the election
The Brotherhood has to field its candidates as independents because the government refuses to recognise the group as an official party, a position the US says it respects.
The voting on Wednesday will be for 127 seats in the Nile Delta, Sohag and Aswan in southern Egypt, the Red Sea coast and the Sinai peninsula - wherever no candidate won more than 50% of the vote last week.
Of those seats, 35 will be contested by Brotherhood candidates. The group has said it expects to win 15 to 20 more seats. The group had just 15 seats when the last parliament's term ended.
Secular groups lagging
Secular opposition parties have been the biggest losers, gaining only a handful of seats and leaving Mubarak's National Democratic Party (NDP) on the verge of winning two-thirds to retain control of the constitution.
A two-thirds majority for the NDP could be important if the government tries to change the system for presidential elections.
Gamal Mubarak leads the policies
committee of the ruling party
This year's constitutional change, allowing Egypt's first contested presidential race in September, makes it almost impossible for a rival to stand against the NDP candidate in 2011.
Critics say the NDP aims to smooth the way for a constitutionally legitimate succession by Mubarak's 41-year-old son Gamal, a senior official of the ruling party. The NDP denies this.
Some seats are being contested on Wednesday by two NDP candidates after some independents, who had originally quit the NDP to run, were reclassified as NDP members again.
Wednesday's vote will be the last round, although three constituencies have not voted because of legal disputes.