Chanting "Allahu Akbar!" ("God is greatest!") and "One point, One demand: Atheists must be hanged", activists from the hardline Hefajat-e-Islam marched along at least six highways, blocking transport between Dhaka and other cities.
Police said about 200,000 people had marched to central Dhaka, where fierce clashes erupted between thousands of rock-throwing protesters and security officials, with police beating back demonstrators with batons.
"At least 100,000 protesters," blocked the road at Tongi town, which connects Dhaka with the northern region, local police chief Ismail Hossain told AFP.
Witnesses said rioting broke out after police tried to intercept stick-wielding protesters, most travelling from remote villages, in front of the country's largest mosque. Trouble then spread to central districts of Dhaka.
Police inspector Mozammel Haq said three dead were brought to Dhaka Medical College and seven others taken to two private clinics including six at the Al Baraka Hospital.
"All six have bullet wounds in their heads," Al Baraka administrative officer Shahjahan Siraj told AFP by telephone.
Police would only say rubber bullets were used in the clashes, but witnesses and local media said hundreds of live rounds were fired by security forces to disperse the rampaging Islamists, who torched a police station, scores of vehicles and shops.
Dozens of small bombs exploded, leaving smoke hanging in the air around the mosque as clashes continued late Sunday night.
One policeman suffered serious head injuries after he was beaten by protesters, according to an AFP correspondent at the scene.
M Adnan, an emergency doctor at Islami Bank Hospital, told AFP nearly 300 protesters were treated in its two branches.
A senior police officer who declined to be named told AFP between "150,000 and 200,000 demonstrators" marched to Motijheel, Dhaka's main commercial district, where they continued to rally even after midnight.
"This government does not have faith in Allah. This is an atheist government, we will not allow them to live in Bangladesh. Muslims are brothers, we must protect Islam," one protester was seen chanting.
The protest was staged as the country was recovering from its worst industrial disaster, which saw at least 620 people killed when a factory building collapsed just outside the capital on April 24.
Hefajat, a newly created radical Islamist group, is demanding the death penalty for those who defame Islam.
It said it staged the mass protest to push a 13-point list of demands, which also include a ban on men and women mixing freely together and the restoration of pledges to Allah in the constitution.
Hefajat leaders have threatened to launch a campaign to oust the government unless their demands are met.
The rally was the latest in a series of mass actions by Hefajat, unusual in Bangladesh because of the large numbers of people taking part.
Last month hundreds of thousands of Hefajat activists demanding a blasphemy law gathered in Dhaka, in what experts said was the largest political rally in decades.
Critics have branded Hefajat's demands a charter for turning Bangladesh into a Taliban-ruled Afghanistan. Women workers including female garment labourers have vented their anger at the group's call to segregate the sexes.
Prime Minister Sheikh Hasina, who has been leading a secular government in the Muslim-majority country since 2009, has rejected the demand for a blasphemy law, saying the existing laws were enough to prosecute blasphemers.
Hasina's ruling Awami League party has accused Hefajat, which draws support from tens of thousands of Islamic seminaries, of being a pawn of the opposition, which lent moral support to Sunday's blockade.
Hardline Islamist groups accuse Hasina's government of trying to intimidate the opposition through a series of trials for war crimes allegedly committed during the 1971 war of independence.
Three Islamists have so far been convicted and two of them were sentenced to death. More than 100 people have been killed during protests over the trials since January this year.