Seats in the Lebanese parliament are divided equally between Muslims and Maronite Christians and key cabinet posts are reserved for members of the major communities.
The country's president must be Christian, the prime minister Sunni and the speaker of parliament Shia.
Lebanon is home to 18 religious sects, and is deeply divided between Christians and Muslims.
"We cannot live in a country where they divide the chairs of ministers according to their confessions, not their merits"
Its sectarian system was soldified in a 1943 national accord in a bid to avoid religious conflict, but the country was torn apart by a brutal 15 year civil war that started in 1975.
The agreement that ended the conflict called for the abolition of sectarianism, but the system has endured.
Under the complicated rules, public sector jobs are subject to religious quotas that change year-on-year in a bid to maintain the delicate balance.
Civil marriage is not recognised under the system, and Lebanese seeking to marry outside their sect are forced to choose between a church or a mosque, or else travel to nearby countries like Cyprus to obtain a civil marriage.
The rally was organised by the grassroots movement Laique Pride using social networking sites.
Said Shaito, one of the organisers, told Al Jazeera that they want equality for all Lebanese citizens.
"We are for citizenship, which is being Lebanese, not Muslim or Christian," he said. "We want people to talk about it, to create a public debate in Lebanon."