Clashes occurred in various parts of the two provinces where polling was held in 20 districts in the first stage of the three-phase polls.
"The armed clash took place in Daraza Sharif Union Council in Khairpur," police officer Pir Muhammad Shah said.
The clash took place between two groups supporting the Pakistan Peoples Party and Pakistan Muslim League functional and they belonged to the Junejo tribe.
He said while 12 people were killed in the armed clashes around 16 were also injured and taken to hospitals.
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There were also clashes and skirmishes between the supporters of the Pakistan Muslims League-Nawaz and Pakistan Tehreek-e-Insaaf.
Punjab government spokesman Zaim Qadri said 200 people were arrested for trouble making and violence.
In unofficial results announced last night, PML-N had taken an early lead on as many as 532 seats, out of a total of 2,696, in Punjab with the Pakistan Tehreek-i-Insaf was a distant second with a lead in 80 constituencies.
In Sindh, the PPP was leading on 564 seats, out of a total of 1,072, while the Muslim League-Functional was ahead on 50 seats.