Although they weren't leading the protests that pushed out the last corrupt government, they've been around for a long time and have a solid ground game. Mubarak's government gave its best effort to shut down the Muslim Brotherhood but it was a losing battle for Mubarak.
Whoever wins in Egypt is likely to be less friendly with the US though the last regime was less friendly with the population of Egypt. Will the Muslim Brotherhood change once they come to power and the billions of US dollars is waved in front of them? That has been known to have its impact on governments, just as it does at home. Al Jazeera:
Early on Friday morning, the Brotherhood, the country's most powerful political force, announced that its candidate was in the lead, followed by a divisive former civil aviation minister more closely tied to Mubarak than anyone else in the race.
However, the overall picture will not be clear for some time. The presidential election commission did not plan to release official results until Tuesday.
If no one wins more than half the votes needed for outright victory in the first round, the top two candidates will contest a June 16 and 17 run-off.
The Brotherhood's estimate was based on results from 236 of roughly 13,000 polling stations. Campaigns were allowed to station observers in the polls throughout the voting and counting process, and the Brotherhood had placed staff in nearly each one.