Four people including a child were killed in clashes in south Yemen between security forces and separatists, who seized half the polling stations in the city of Aden to prevent voting on Tuesday.
Gunmen from the Southern Movement, meanwhile, opened fire on a polling booth in Aden's Crater neighbourhood, as British House of Lords member Baroness Emma Nicholson was visiting, a security official said adding that she was not harmed.
The attack came despite a heavy security detail accompanying Nicholson's every movement in the city, witnesses said.
One Yemeni soldier was wounded in the attack, said the official.
Activists from the Southern Movement, who say the election fails to meet their aspirations for autonomy or southern independence, have boycotted the referendum in which Vice President Abdrabuh Mansur Hadi is the sole consensus candidate.
But some hardline factions have vowed to mark Tuesday's presidential vote as a day of "civil disobedience" to prevent voters from casting their ballots.
In Aden, the main southern city, a 10-year-old child was killed when separatist militants traded gunfire with police near the election commission headquarters in the Dar Saad neighbourhood, residents and medics said.
In Aden's Mansura neighbourhood, a stronghold of the Southern Movement, gunmen killed a policeman. Several other people were wounded in ongoing clashes between separatist militants and troops throughout the city.
In the southeastern town of Mukala, separatists attacked a polling station killing a soldier, a military official said.
"Gunmen from the Southern Movement tried to storm a polling station" in the capital of Hadramawt province "killing a soldier," the official said, adding that two gunmen were wounded in the assault.
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In Lahij province, a protester was killed and two others were wounded in clashes between hardline southern militants and security forces, activists from the movement said.
"Security forces shot dead Fadhel Naser Badie who was among a group of demonstrators gathered outside a polling station in protest against the elections in Huta," one activist said.
Two other protesters were wounded in the same attack, he added.
By mid-day Tuesday, separatists had seized half of Aden's polling stations.
"Half of the polling booths in Aden have been shut down after they were seized by gunmen from the Southern Movement," a local government official told AFP. He said 10 out of the city's 20 voting stations were closed due to the violence.
According to witnesses, militants stormed the booths and confiscated ballot boxes as security forces, which were deployed to guard the stations, withdrew from their posts.
Officials said earlier that a total of 103,000 soldiers were deployed to guard polling stations.
Militants also used rocks to block roads and set tyres on fire to disrupt the movement of people in Aden, where at least one polling station was set ablaze, witnesses said. No casualties were reported.
Residents in Yemen's formerly independent south complain of discrimination by the Sanaa government, citing an inequitable distribution of resources since the union between north and south in 1990.
The south broke away again in 1994, sparking a brief civil war that ended with the region being overrun by northern troops.
Hadi, himself a southerner, will lead Yemen during a two-year interim period as stipulated in a Gulf-brokered deal signed by President Ali Abdullah Saleh in November after months of protests against his 33-year iron-fisted rule.