Aung San Suu Kyi, the long-time standard-bearer for democracy in Burma, is taking a leap of faith in running for parliament today, opting to enter a political system crafted and run by the soldiers who kept her locked up for a total of 15 years.

Her party's participation in this weekend's by-elections for 45 seats marks a change of heart for the Nobel Peace Prize winner, who repeatedly rebuffed the military's attempts to bring her into a political apparatus in which it dictated the terms.

But since a general election in November 2010, and Suu Kyi's release from house arrest the same month, the pace of change under a nominally civilian government has been staggering – enough, apparently, to convince her to compromise with the apparently reform-minded ex-generals now in charge.

However, some Burmese fear it is a deal with the devil, given the continuing presence of the military in political life.

Suu Kyi, 66, is keeping an open mind. She said recently: "Some are a little bit too optimistic about the situation. We are cautiously optimistic. We are at the beginning of a road. Many people are beginning to say that the democratisation process here is irreversible. It's not so."

Without her National League for Democracy (NLD) party's participation, there would have been little interest in today's by-elections for a legislature where 25% of the seats are reserved for the military and a party close to the military has most of the rest.

But the polls have captured the world's imagination and, if they are deemed free and fair, could persuade the West to start to lift economic sanctions imposed under the junta.

Suu Kyi is running in the constituency of Kawhmu, south of Rangoon. She was due there yesterday evening and planned to tour polling stations early today.

However, campaigning has left Suu Kyi suffering from sickness and exhaustion and she remains "a little delicate," she said on Friday.

Suu Kyi has made no secret of the fact she wants to change a constitution that enshrines the military's role in politics.

"There are certain laws which are obstacles to the freedom of the people," she said during a rally. "We will strive to abolish these laws within the framework of the parliament."

That puts her on a collision course with hardliners and an armed forces commander who has vowed to protect the military's place in the corridors of power.

This is only the third election Burma has held since 1962, when the military seized power. The most recent, in 1990, was won by the NLD, but the junta annulled the results. Two decades later the NLD boycotted an election that was widely criticised as rigged, but nevertheless brought to power a quasi-civilian, reform-minded government.

Yesterday, Suu Kyi spoke of irregularities ahead of today's by-election that went "beyond what is acceptable for democratic elections".

In the constituency she is contesting, the names of hundreds of deceased had been listed on the electoral roll, while those of more than 1300 people eligible to vote were missing, her party said.

Suu Kyi also cited cases of intimidation and vandalism of campaign materials. A small number of representatives from the Association of South-East Asian Nations, plus the European Union and US, have been invited to observe polling.