The group had failed to win any seats outright in the first round of voting and that just 21 of its 130 candidates were sure of making it into next Sunday's second-round run-offs.
The Brotherhood is forced to field its candidates as independents to get round a ban on religious parties. In the last parliament it held 88 seats in the 518 parliament.
In the run-up to Sunday's vote, the Islamists were targeted in a systematic crackdown by the authorities, which saw at least 1,200 of its supporters arrested, more than a dozen candidates disqualified and 11 members sentenced to two years in jail for campaigning and handing out leaflets.
Egypt expert Kristina Kausch at the Madrid based FRIDE says the Muslim Brotherhood was considered to be the strongest opposition party but this was not reflected in the vote.
“The newer, more dynamic opposition parties all boycott these elections and the few who don’t are the old, co-opted opposition parties that have a good relationship with the regime but don’t actually have a stronghold in the population,” said Kausch.
“But these latter are expected to be the stronger opposition party in the parliament which is a clear sign that these elections are rigged.”
Final results from the first round were not expected before Tuesday but initial indications showed the ruling National Democratic Party (NDP) of President Hosni Mubarak had made large gains.