The Islamist group also is facing internal discord, with a handful of young members breaking away. Some say they disapprove of its rigid top-down leadership structure and its politics.
The organization, which has social and political wings, has the support of an estimated 20 percent of Egypt's mostly Muslim population. Until now it has been the only counterweight to Mubarak's ruling party.
"In light of the oppression of Mubarak, the group was cohesive, one body," said Abdel Moneim Mahmoud, a former member and Egyptian journalist who writes about Islamic politics. "Now there is freedom. Many ideas will come to the surface and break some of that cohesion."
Secular Egyptians and many in the West view the Brotherhood warily because it seeks to deepen the role of Islam in people's lives. Deeply religious Egyptians, meanwhile, view it as too liberal.
The foray of the Brotherhood and other Islamist groups into mainstream politics, and the competition among them, is certain to stoke debate about the intersection between religion and governance in a country that has been ruled in a secular way for decades.
Since Mubarak's ouster, the Brotherhood has offered few signs that it aspires to transform Egypt into a repressive Islamic state. The group bills itself as a moderate movement that seeks to broaden the appeal of Islam from the ground up. It also has long lobbied for a democratic system that ensures freedom of expression and term limits.
Brotherhood leaders say that they will not field a candidate for the presidency this year, and that they intend to compete for no more than a quarter of the seats in the next parliament.
"It's not our aim to take power, it is just to participate," said Abdel Moneim Abou el-Fotouh, a prominent member of the Brotherhood who is regarded as progressive.
Members and political analysts say the Brotherhood is deliberately keeping a low profile because its leaders are concerned that showing more ambition could backfire by stirring fear in the West and among secular Egyptians.
"You don't know if what they say is what they want, and that's the big concern," a Western diplomat said, speaking on condition of anonymity to voice an emerging concern.
The opening of Egyptian politics is bringing to the fore long-standing rifts among conservative and progressive factions within the Brotherhood. Women and young members for years have lobbied for more prominent roles within the organization.
Until now, those who left the group found it nearly impossible to create new political organizations because Mubarak's government crushed emerging opposition movements.
In the past, only the Brotherhood and Mubarak's National Democratic Party were able to turn out voters, said Elijah Zarwan, a Cairo-based senior analyst with the International Crisis Group, a think tank.