Although the two largest sub-groups of Islam share much in common and for the most part have lived peacefully alongside each other, their differences have often boiled over into open confrontation.
Nowhere has this been more true than in Pakistan where some 30 million Shias reside as a minority among the country's 120 million Sunnis.
For the first 30 years of Pakistan's history the tensions remained under the surface, overshadowed by the threat of a common enemy, India.
But the stresses have come to the fore since the 1980s when then military dictator General Zia al-Haq courted sectarian Sunni scholars to build up a political base.
A defining moment was the establishment of the Sipah-i-Sahaba in 1985. The name means the Party of the Prophet's Companions and reflects the group's raison d'etre.
The Sunni-Shia split centres on which of the Prophet Muhammad's companions should have succeeded him.
The Sunni accuse the Shia of reviling the first three successors in arguing that the fourth caliph of Islam, Ali, was the chosen one.
The Sipah-i-Sahaba was dedicated to the establishment of Pakistan as a Sunni state and originally pursued its mission with ruthless attacks on Shia leaders and laypersons. Shia mosques have been a favourite target.
At its height the party could boast a strength of 100,000 loyal cadres and was believed to be financed with the help of clandestine branches in expatriate communities in the Middle East and West.
Not surprisingly Sunni sectarianism provoked a similar reaction in the Shia community, already buoyed by the coming to power of Ayat Allah Khomeini's Shia government in neighbouring Iran.
Global issues have brought Sunni
and Shia communities together
Initially a non-violent party, the Tehrik-e-Jafria Pakistan soon fragmented with more hardline groups waging a bloody campaign against their Sunni rivals, assassinating three leaders of the Sipah-i-Sahaba, the last of them in October 2003.
Since 1980 some 4000 people have died in sectarian attacks in Pakistan, perpetrated by splinter groups of the Sipah-i-Sahaba and Tehrik-i-Jafaria. The most violent of the Sunni groups has been the Lashkar-i-Jhangvi, named after the founder of the Sipah-i-Sahaba, Haq Nawaz Jhangvi.
In March, 44 people were killed and 150 wounded in an attack on a Shia religious procession in the southwestern city of Quetta that was blamed on Sunni extremists.
And 20 Shia died when a bomber blew himself up in a Karachi mosque earlier this month.
The bloodshed has caused horror among clerics on both sides.
They have sought to smooth over differences by shifting the focus from each other to the greater problems facing Pakistan such as its role in the US-led war on terror, and the continuing absence of democracy under General Musharraf's dictatorship.
An alliance of religious parties, the Muttahida Majlis-i-Amal, stormed to power in the Pakistani North West Frontier Province in parliamentary elections in 2002.
The MMA contains both elements of Shia and Sunni groups, including the Sipah-i-Sahaba and Tehrik-i-Jafaria in their new tamer manifestations.
But the parties' convergence at the political level been overshadowed by the ever more extreme activities of their various offshoots making it hard for Pakistan to shake off its reputation for ethnic and sectarian intolerance.