Some had walked for more than 12 days, from Iraq's far south or across the border from Iran, while others were bused in or crammed into lorries for the journey.
Defence Minister Khaled al-Obeidi said a total of 17 million will have gone through Karbala for Arbaeen this year, including more than four million foreigners from 60 countries.
A sea of devotees descended on the city to reach the shrine of Imam Hussein, beating their heads and chests to show remorse for not saving him from the armies of the caliph Yazid that killed and beheaded him in 680 AD.
A mortar attack that killed one person on Friday highlighted the huge security concerns surrounding what is believed to be one of the largest religious gatherings in the world.
But the pilgrims were undeterred.
"Forget mortars, even if it rains jihadists on Karbala, we will not be prevented from visiting the Imam Hussein shrine," said Kadhem Hussein, a 25-year-old who had walked from Nasiriyah, some 300 kilometres away.
The Islamic State group -- led by Sunni extremists -- considers Shiites to be heretics and has made targeting the community one of its main objectives.
Many of the million or so Iranians who flocked to Iraq for the occasion said they were performing the pilgrimage on the order of their nation's supreme leader, Ayatollah Ali Khamenei.
Turnout estimates were hard to verify independently but all officials seemed to agree this Arbaeen was the largest they had ever seen.
The local operations command chief said new access roads had to be opened to handle the flow of pilgrims converging on Karbala, a medium-sized city around 70 kilometres south of Baghdad.
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