Routes leading to Kadhimiyah neighbourhood, site of the shrine of Imam Musa Kadhim, the seventh of 12 Shiite imams who died in 799, were closed to all traffic except emergency vehicles, AFP journalists said.
Pilgrims wound under a blistering sun through the streets in their thousands, repeating religious chants, some beating their chests in a sign of mourning for the imam.
Tents along the way provided the pilgrims with free food and water.
In the Utayfiyah area of north Baghdad, long lines of pilgrims, many wearing green headbands and some carrying green flags, the colour of Islam, were seen marching toward the shrine.
Vast crowds of chanting pilgrims were also seen walking through Karrada in central Baghdad, where a bomb on Wednesday blasted the pilgrims` food tents, killing 16 people, damaging cars and scattering human remains across the street.
Another car bomb exploded on the outskirts of Kadhimiyah, killing seven people, leaving a hole two metres (yards) deep in a street, damaging cars and destroying a number of makeshift houses.
Coordinated attacks took place right across Iraq on Wednesday, leaving a total of 72 people and more than 250 wounded, and marking the deadliest day in the country in almost ten months.
Along with the security forces, the Shiite majority in Iraq has been a main target of Sunni Arab armed groups since the US-led invasion of 2003 toppled now executed dictator Saddam Hussein`s Sunni-dominated regime.
Violence across Iraq has declined dramatically since the 2006-2007 peak but attacks remain common, especially in Baghdad. A total of 132 Iraqis were killed in May, official figures show.