The Brotherhood, banned since 1954, has more than doubled its strength in parliament in the first stage of voting, making the most of leeway from the government to show the weight of political Islam as Egypt's strongest opposition force.
The officially banned but tolerated group made significant gains in Alexandria, Aljazeera's correspondent in Egypt reported.
Two of its candidates in Minya al-Basal and a third, Sayyid Askar, in Tanta have been declared winners, Aljazeera's correspondent said, while governing National Democratic Party (NDP) candidates have won four to six seats in parliament.
Police arrested about 470 activists affiliated to the Brotherhood during and before voting on Sunday for the legislative elections. Police and armed gangs blocked polling stations in some Muslim Brotherhood strongholds, witnesses told agency reporters.
Hussain Abd al-Ghani, Aljazeera's Egypt bureau chief, reporting from Cairo, said the Muslim Brotherhood's success in the second round matches those made by it in the first-round runoff.
The Brotherhood won four seats during the first round, 30 in the first-round runoff, and the group's sources told Aljazeera that 14 candidates have won in the second round in nine governorates.
Driver Muhammad Khalil Ibrahim
was killed in Alexandria
At least 35 of the group's candidates will re-run in the second-round runoff, Abd al-Ghani said.
The group's victories were primarily in Alexandria, al-Gharbiya, al-Ismailiya and al-Qalyubiya governorates, the correspondent said.
Brotherhood parliamentarians from Alexandria, Hussain Muhammad and Hamdi Hasan, have retained their seats, said Samir Omar, an Aljazeera correspondent reporting from Alexandria.
Sunday's polling was marred by widespread violence, which claimed the first victim of the elections, the driver of a candidate whom independent monitoring groups said was beaten to death by NDP thugs.
Alexandria was the scene of battles between supporters of rival candidates, as clans fought with sticks, knives and guns.
"Who can hit the hardest?" was the headline of Egypt's leading independent daily Al-Masri Al-Yom, which carried front-page pictures of men and teenagers wielding swords and a candidate holding a handgun.
"The success recorded by the Muslim Brothers during the first phase sparked fear in the regime, which cannot bear the presence of opposition in parliament," the Islamist movement's number two Mohammed Habib told AFP.
"The NDP could see it was going to lose and resorted to violence and thugs against the Muslim Brotherhood. All this was aimed at preventing people from voting," he added.
Brotherhood loyalists clash with
NDP supporters in Alexandria
Activists overseeing the elections told Aljazeera that the second round was bloodier and more violent than the first-round runoff.
But the Interior Ministry said the performance of the security services "was characterised by neutrality" and put the blame for the violence squarely on the Brotherhood's shoulders.
"The supporters of some candidates, the majority of which were Islamists, engaged in thuggery, voter intimidation and violence," it said in a statement.
Ruling party not threatened
The Brotherhood is contesting one-third of the chamber's seats and does not pose a threat to the NDP's control of parliament.
Official results have yet to be released, and it was not clear how many seats the NDP had won.
The ruling party won 68 of 164 seats in the first round, while the Brotherhood won 21%. Secular opposition parties won only a handful of places.
The third and final stage of voting, for 136 seats, starts on 1 December.