He was detained after going to join a fresh "walk-to-walk" protest against rising living costs. At least 12 other opposition leaders were arrested too.
The opposition campaign began last week and spread to several towns, at least three people were killed in clashes.
At the weekend, the president described the campaign as "idiotic" and illegal.
Correspondents say the government is desperate to ensure that large street protests do not take place.
Last week it tried to block popular social network sites on the internet.
Dr Besigye, who was arrested and shot in the hand in protests last week, lost to President Yoweri Museveni in February's election but says the poll was rigged.
He has been defeated by Mr Museveni in three presidential elections, gaining 26% to the president's 68% in February.
'Take a walk'
Dr Besigye was detained as he set out on foot from his home in the capital, Kampala, to join the walk-to-work protest.
The BBC's Joshua Mmali in Kampala says plain-clothed security men picked him up off a dirt road near his house, keen to make sure he did not reach the main tarmac highway.Kizza Besigye was shot in the hand last week
The Forum for Democratic Change leader was taken to the Kasangati police station on the outskirts of the capital where his supporters gathered to protest.
The police and army fought running battles with the protesters, shooting in the air and using tear gas.
Rioters who were pelting passing cars with stones were also arrested.
Elsewhere in Kampala, Democratic Party leader Norbert Mao was arrested shortly after he left his house.
Uganda People's Congress party president, Olara Otunu, participating in the protest for the first time, has also been arrested.
Dr Besigye was charged with inciting violence and causing rioting and was later released on bail - for a second time in a week.
As he left the court, he pledged to continue the protest against rising fuel and food prices this coming Thursday - as part of plans by the opposition to walk to work twice a week.
At a press conference on Saturday, President Museveni warned against further demonstrations.
He insists his government cannot intervene to bring down the price of fuel and food commodities, because high food prices are good for farmers, our correspondent says.
"We made it clear to Besigye that you are not going to demonstrate or to walk," he said, according to AFP news agency.
"If you want to walk, go somewhere and take a walk."
Before February's election, Dr Besigye had called for Egypt-style uprisings in the event of fraud.
The police responded by banning public demonstrations.
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